jsongrapher 2.8__py3-none-any.whl → 3.7__py3-none-any.whl

JSONGrapher/JSONRecordCreator.py

@@ -1,4 +1,6 @@
 import json
+import JSONGrapher.styles.layout_styles_library
+import JSONGrapher.styles.trace_styles_collection_library
 #TODO: put an option to suppress warnings from JSONRecordCreator
 
 
@@ -48,21 +50,22 @@ def add_records_to_global_records_list_and_plot(all_selected_file_paths, newly_a
 #This ia JSONGrapher specific wrapper function to drag_and_drop_gui create_and_launch.
 #This launches the python based JSONGrapher GUI.
 def launch():
-    #Check if we have the module we need. First try with package, then locally.
     try:
         import JSONGrapher.drag_and_drop_gui as drag_and_drop_gui
-    except:
-        #if the package is not present, or does not have it, try getting the module locally.
-        import drag_and_drop_gui
-    selected_files = drag_and_drop_gui.create_and_launch(app_name = "JSONGRapher", function_for_after_file_addition=add_records_to_global_records_list_and_plot)
-    #We will not return the selected_files, and instead will return the global_records_list.
+    except ImportError:
+        try:
+            import drag_and_drop_gui  # Attempt local import
+        except ImportError as exc:
+            raise ImportError("Module 'drag_and_drop_gui' could not be found locally or in JSONGrapher.") from exc
+    _selected_files = drag_and_drop_gui.create_and_launch(app_name = "JSONGrapher", function_for_after_file_addition=add_records_to_global_records_list_and_plot)
+    #We will not return the _selected_files, and instead will return the global_records_list.
     return global_records_list
 
 ## End of the portion of the code for the GUI##
 
 
 #the function create_new_JSONGrapherRecord is intended to be "like" a wrapper function for people who find it more
-# intuitive to create class objects that way, this variable is actually just a reference 
+# intuitive to create class objects that way, this variable is actually just a reference
 # so that we don't have to map the arguments.
 def create_new_JSONGrapherRecord(hints=False):
     #we will create a new record. While we could populate it with the init,
@@ -72,23 +75,34 @@ def create_new_JSONGrapherRecord(hints=False):
         new_record.add_hints()
     return new_record
 
+#This is actually a wrapper around merge_JSONGrapherRecords. Made for convenience.
+def load_JSONGrapherRecords(recordsList):
+    return merge_JSONGrapherRecords(recordsList)
+
+#This is actually a wrapper around merge_JSONGrapherRecords. Made for convenience.
+def import_JSONGrapherRecords(recordsList):
+    return merge_JSONGrapherRecords(recordsList)
 
 #This is a function for merging JSONGrapher records.
 #recordsList is a list of records 
 #Each record can be a JSONGrapherRecord object (a python class object) or a dictionary (meaning, a JSONGrapher JSON as a dictionary)
 #If a record is received that is a string, then the function will attempt to convert that into a dictionary.
 #The units used will be that of the first record encountered
+#if changing this function's arguments, then also change those for load_JSONGrapherRecords and import_JSONGrapherRecords
 def merge_JSONGrapherRecords(recordsList):
+    if type(recordsList) == type(""):
+        recordsList = [recordsList]
     import copy
     recordsAsDictionariesList = []
     merged_JSONGrapherRecord = create_new_JSONGrapherRecord()
     #first make a list of all the records as dictionaries.
     for record in recordsList:
-        if type(record) == type({}):
+        if isinstance(record, dict):#can't use type({}) or SyncedDict won't be included.
             recordsAsDictionariesList.append(record)
         elif type(record) == type("string"):
-            record = json.loads(record)
-            recordsAsDictionariesList.append(record)
+            new_record = create_new_JSONGrapherRecord()
+            new_fig_dict = new_record.import_from_json(record)
+            recordsAsDictionariesList.append(new_fig_dict)
         else: #this assumpes there is a JSONGrapherRecord type received. 
             record = record.fig_dict
             recordsAsDictionariesList.append(record)
@@ -128,8 +142,30 @@ def merge_JSONGrapherRecords(recordsList):
             #now, add the scaled data objects to the original one.
             #This is fairly easy using a list extend.
             merged_JSONGrapherRecord.fig_dict["data"].extend(scaled_fig_dict["data"])
+    merged_JSONGrapherRecord = convert_JSONGRapherRecord_data_list_to_class_objects(merged_JSONGrapherRecord)
     return merged_JSONGrapherRecord
 
+def convert_JSONGRapherRecord_data_list_to_class_objects(record):
+    #will also support receiving a fig_dict
+    if isinstance(record, dict):
+        fig_dict_received = True
+        fig_dict = record
+    else:
+        fig_dict_received = False
+        fig_dict = record.fig_dict
+    data_list = fig_dict["data"]
+    #Do the casting into data_series objects by creating a fresh JSONDataSeries object and populating it.
+    for data_series_index, data_series_received in enumerate(data_list):
+        JSONGrapher_data_series_object = JSONGrapherDataSeries()
+        JSONGrapher_data_series_object.update_while_preserving_old_terms(data_series_received)
+        data_list[data_series_index] = JSONGrapher_data_series_object
+    #Now prepare for return.
+    if fig_dict_received == True:
+        fig_dict["data"] = data_list
+        record = fig_dict
+    if fig_dict_received == False:
+        record.fig_dict["data"] = data_list
+    return record
 
 ### Start of portion of the file that has functions for scaling data to the same units ###
 #The below function takes two units strings, such as
@@ -168,12 +204,22 @@ def get_units_scaling_ratio(units_string_1, units_string_2):
         #While it may be possible to find a way using the "Q" objects directly, this is the way I found so far, which converts the U object into a Q object.
         units_object_converted = 1*unitpy.U(units_string_1)
         ratio_with_units_object = units_object_converted.to(units_string_2)
-    except: #the above can fail if there are reciprocal units like 1/bar rather than (bar)**(-1), so we have an except statement that tries "that" fix if there is a failure.
+    #the above can fail if there are reciprocal units like 1/bar rather than (bar)**(-1), so we have an except statement that tries "that" fix if there is a failure.
+    except Exception as general_exception: # This is so VS code pylint does not flag this line. pylint: disable=broad-except, disable=unused-variable
         units_string_1 = convert_inverse_units(units_string_1)
         units_string_2 = convert_inverse_units(units_string_2)
         units_object_converted = 1*unitpy.U(units_string_1)
-        ratio_with_units_object = units_object_converted.to(units_string_2)
+        try:
+            ratio_with_units_object = units_object_converted.to(units_string_2)
+        except KeyError as e: 
+            raise KeyError(f"Error during unit conversion in get_units_scaling_ratio: Missing key {e}. Ensure all unit definitions are correctly set. Unit 1: {units_string_1}, Unit 2: {units_string_2}") from e
+        except ValueError as e:
+            raise ValueError(f"Error during unit conversion in get_units_scaling_ratio: {e}. Make sure unit values are valid and properly formatted. Unit 1: {units_string_1}, Unit 2: {units_string_2}") from e       
+        except Exception as e:  # pylint: disable=broad-except
+            raise RuntimeError(f"An unexpected error occurred in get_units_scaling_ratio when trying to convert units: {e}. Double-check that your records have the same units. Unit 1: {units_string_1}, Unit 2: {units_string_2}") from e
+
     ratio_with_units_string = str(ratio_with_units_object)
+
     ratio_only = ratio_with_units_string.split(' ')[0] #what comes out may look like 1000 gram/(meter second), so we split and take first part.
     ratio_only = float(ratio_only)
     return ratio_only #function returns ratio only. If function is later changed to return more, then units_strings may need further replacements.
@@ -183,7 +229,7 @@ def return_custom_units_markup(units_string, custom_units_list):
     sorted_custom_units_list = sorted(custom_units_list, key=len, reverse=True)
     #the units should be sorted from longest to shortest if not already sorted that way.
     for custom_unit in sorted_custom_units_list:
-        units_string.replace(custom_unit, '<'+custom_unit+'>')
+        units_string = units_string.replace(custom_unit, '<'+custom_unit+'>')
     return units_string
 
     #This function tags microunits.
@@ -235,7 +281,7 @@ def add_custom_unit_to_unitpy(unit_string):
     # and for the new entry, it will also return a special NoneType that we can't easy check.
     # the structer unitpy.ledger.units is a list, but unitpy.ledger._lookup is a dictionary we can use
     # to check if the key for the new unit is added or not.
-    if unit_string not in unitpy.ledger._lookup:
+    if unit_string not in unitpy.ledger._lookup:  #This comment is so the VS code pylint does not flag this line. pylint: disable=protected-access
         unitpy.ledger.add_unit(new_entry) #implied return is here. No return needed.
 
 def extract_tagged_strings(text):
@@ -273,11 +319,11 @@ def scale_fig_dict_values(fig_dict, num_to_scale_x_values_by = 1, num_to_scale_y
     #iterate across the data objects inside, and change them.
     for data_index, dataseries in enumerate(scaled_fig_dict["data"]):
         dataseries = scale_dataseries_dict(dataseries, num_to_scale_x_values_by=num_to_scale_x_values_by, num_to_scale_y_values_by=num_to_scale_y_values_by)
-        scaled_fig_dict[data_index] = dataseries #this line shouldn't be needed due to mutable references, but adding for clarity and to be safe.
+        scaled_fig_dict["data"][data_index] = dataseries #this line shouldn't be needed due to mutable references, but adding for clarity and to be safe.
     return scaled_fig_dict
 
 
-def scale_dataseries_dict(dataseries_dict, num_to_scale_x_values_by = 1, num_to_scale_y_values_by = 1):
+def scale_dataseries_dict(dataseries_dict, num_to_scale_x_values_by = 1, num_to_scale_y_values_by = 1, num_to_scale_z_values_by = 1):
     import numpy as np
     dataseries = dataseries_dict
     dataseries["x"] = list(np.array(dataseries["x"], dtype=float)*num_to_scale_x_values_by) #convert to numpy array for multiplication, then back to list.
@@ -286,15 +332,233 @@ def scale_dataseries_dict(dataseries_dict, num_to_scale_x_values_by = 1, num_to_
     # Ensure elements are converted to standard Python types. 
     dataseries["x"] = [float(val) for val in dataseries["x"]] #This line written by copilot.
     dataseries["y"] = [float(val) for val in dataseries["y"]] #This line written by copilot.
+
+    if "z" in dataseries:
+        dataseries["z"] = list(np.array(dataseries["z"], dtype=float)*num_to_scale_z_values_by) #convert to numpy array for multiplication, then back to list.
+        dataseries["z"] = [float(val) for val in dataseries["z"]] #Mimicking above lines.
     return dataseries_dict
 
 ### End of portion of the file that has functions for scaling data to the same units ###
 
+## This is a special dictionary class that will allow a dictionary
+## inside a main class object to be synchronized with the fields within it.
+class SyncedDict(dict):
+    """A dictionary that automatically updates instance attributes."""
+    def __init__(self, owner):
+        super().__init__()
+        self.owner = owner  # Store reference to the class instance
+    def __setitem__(self, key, value):
+        """Update both dictionary and instance attribute."""
+        super().__setitem__(key, value)  # Set in the dictionary
+        setattr(self.owner, key, value)  # Sync with instance attribute
+    def __delitem__(self, key):
+        super().__delitem__(key)  # Remove from dict
+        if hasattr(self.owner, key):
+            delattr(self.owner, key)  # Sync removal from instance
+    def pop(self, key, *args):
+        """Remove item from dictionary and instance attributes."""
+        value = super().pop(key, *args)  # Remove from dictionary
+        if hasattr(self.owner, key):
+            delattr(self.owner, key)  # Remove from instance attributes
+        return value
+    def update(self, *args, **kwargs):
+        super().update(*args, **kwargs)  # Update dict
+        for key, value in self.items():
+            setattr(self.owner, key, value)  # Sync attributes
+
+
+class JSONGrapherDataSeries(dict): #inherits from dict.
+    def __init__(self, uid="", name="", trace_style="", x=None, y=None, **kwargs):
+        """Initialize a data series with synced dictionary behavior.
+        Here are some fields that can be included, with example values.
+
+        "uid": data_series_dict["uid"] = "123ABC",  # (string) a unique identifier
+        "name": data_series_dict["name"] = "Sample Data Series",  # (string) name of the data series
+        "trace_style": data_series_dict["trace_style"] = "scatter",  # (string) type of trace (e.g., scatter, bar)
+        "x": data_series_dict["x"] = [1, 2, 3, 4, 5],  # (list) x-axis values
+        "y": data_series_dict["y"] = [10, 20, 30, 40, 50],  # (list) y-axis values
+        "mode": data_series_dict["mode"] = "lines",  # (string) plot mode (e.g., "lines", "markers")
+        "marker_size": data_series_dict["marker"]["size"] = 6,  # (integer) marker size
+        "marker_color": data_series_dict["marker"]["color"] = "blue",  # (string) marker color
+        "marker_symbol": data_series_dict["marker"]["symbol"] = "circle",  # (string) marker shape/symbol
+        "line_width": data_series_dict["line"]["width"] = 2,  # (integer) line thickness
+        "line_dash": data_series_dict["line"]["dash"] = "solid",  # (string) line style (solid, dash, etc.)
+        "opacity": data_series_dict["opacity"] = 0.8,  # (float) transparency level (0-1)
+        "visible": data_series_dict["visible"] = True,  # (boolean) whether the trace is visible
+        "hoverinfo": data_series_dict["hoverinfo"] = "x+y",  # (string) format for hover display
+        "legend_group": data_series_dict["legend_group"] = None,  # (string or None) optional grouping for legend
+        "text": data_series_dict["text"] = "Data Point Labels",  # (string or None) optional text annotations
+
+        """
+        super().__init__()  # Initialize as a dictionary
+
+        # Default trace properties
+        self.update({
+            "uid": uid,
+            "name": name,
+            "trace_style": trace_style,
+            "x": list(x) if x else [],
+            "y": list(y) if y else []
+        })
+
+        # Include any extra keyword arguments passed in
+        self.update(kwargs)
+
+    def update_while_preserving_old_terms(self, series_dict):
+        """Update instance attributes from a dictionary. Overwrites existing terms and preserves other old terms."""
+        self.update(series_dict)
+
+    def get_data_series_dict(self):
+        """Return the dictionary representation of the trace."""
+        return dict(self)
+
+    def set_x_values(self, x_values):
+        """Update the x-axis values."""
+        self["x"] = list(x_values) if x_values else []
+
+    def set_y_values(self, y_values):
+        """Update the y-axis values."""
+        self["y"] = list(y_values) if y_values else []
+
+    def set_name(self, name):
+        """Update the name of the data series."""
+        self["name"] = name
+
+    def set_uid(self, uid):
+        """Update the unique identifier (uid) of the data series."""
+        self["uid"] = uid
+
+    def set_trace_style(self, style):
+        """Update the trace style (e.g., scatter, scatter_spline, scatter_line, bar)."""
+        self["trace_style"] = style
+
+    def set_marker_symbol(self, symbol):
+        self.set_marker_shape(shape=symbol)
+
+    def set_marker_shape(self, shape):
+        """
+        Update the marker shape (symbol).
+
+        Supported marker shapes in Plotly:
+        - 'circle' (default)
+        - 'square'
+        - 'diamond'
+        - 'cross'
+        - 'x'
+        - 'triangle-up'
+        - 'triangle-down'
+        - 'triangle-left'
+        - 'triangle-right'
+        - 'pentagon'
+        - 'hexagon'
+        - 'star'
+        - 'hexagram'
+        - 'star-triangle-up'
+        - 'star-triangle-down'
+        - 'star-square'
+        - 'star-diamond'
+        - 'hourglass'
+        - 'bowtie'
+
+        :param shape: String representing the desired marker shape.
+        """
+        self.setdefault("marker", {})["symbol"] = shape
+
+    def add_data_point(self, x_val, y_val):
+        """Append a new data point to the series."""
+        self["x"].append(x_val)
+        self["y"].append(y_val)
+
+    def set_marker_size(self, size):
+        """Update the marker size."""
+        self.setdefault("marker", {})["size"] = size
+
+    def set_marker_color(self, color):
+        """Update the marker color."""
+        self.setdefault("marker", {})["color"] = color
+
+    def set_mode(self, mode):
+        """Update the mode (options: 'lines', 'markers', 'text', 'lines+markers', 'lines+text', 'markers+text', 'lines+markers+text')."""
+        # Check if 'line' is in the mode but 'lines' is not. Then correct for user if needed.
+        if "line" in mode and "lines" not in mode:
+            mode = mode.replace("line", "lines")
+        self["mode"] = mode
+
+    def set_annotations(self, text): #just a convenient wrapper.
+        self.set_text(text) 
+
+    def set_text(self, text):
+        #text should be a list of strings teh same length as the data series, one string per point.
+        """Update the annotations with a list of text as long as the number of data points."""
+        if text == type("string"): 
+            text = [text] * len(self["x"])  # Repeat the text to match x-values length
+        else:
+            pass #use text directly    
+        self["text"] = text
+
+
+    def set_line_width(self, width):
+        """Update the line width, should be a number, normally an integer."""
+        line = self.setdefault("line", {})
+        line.setdefault("width", width)  # Ensure width is set
+
+    def set_line_dash(self, dash_style):
+        """
+        Update the line dash style.
+
+        Supported dash styles in Plotly:
+        - 'solid' (default) → Continuous solid line
+        - 'dot' → Dotted line
+        - 'dash' → Dashed line
+        - 'longdash' → Longer dashed line
+        - 'dashdot' → Dash-dot alternating pattern
+        - 'longdashdot' → Long dash-dot alternating pattern
+
+        :param dash_style: String representing the desired line style.
+        """
+        self.setdefault("line", {})["dash"] = dash_style
+
+    def set_transparency(self, transparency_value):
+        """
+        Update the transparency level by converting it to opacity.
+
+        Transparency ranges from:
+        - 0 (completely opaque) → opacity = 1
+        - 1 (fully transparent) → opacity = 0
+        - Intermediate values adjust partial transparency.
+
+        :param transparency_value: Float between 0 and 1, where 0 is opaque and 1 is transparent.
+        """
+        self["opacity"] = 1 - transparency_value
+
+    def set_opacity(self, opacity_value):
+        """Update the opacity level between 0 and 1."""
+        self["opacity"] = opacity_value
+
+    def set_visible(self, is_visible):
+        """Update the visibility of the trace.
+            "True" → The trace is fully visible.
+            "False" → The trace is completely hidden.
+            "legendonly" → The trace is hidden from the plot but still appears in the legend.
+        
+        """
+        
+        self["visible"] = is_visible
+
+    def set_hoverinfo(self, hover_format):
+        """Update hover information format."""
+        self["hoverinfo"] = hover_format
+
+
+
 class JSONGrapherRecord:
     """
     This class enables making JSONGrapher records. Each instance represents a structured JSON record for a graph.
     One can optionally provide an existing JSONGrapher record during creation to pre-populate the object.
-    One can also manipulate the fig_dict inside, directly, using syntax like Record.fig_dict["comments"] = ...
+    One can manipulate the fig_dict inside, directly, using syntax like Record.fig_dict["comments"] = ...
+    One can also use syntax like Record["comments"] = ...  as some 'magic' synchronizes fields directlyin the Record with fields in the fig_dict.
+    However, developers should usually use the syntax like Record.fig_dict, internally, to avoid any referencing mistakes.
+
 
     Arguments & Attributes (all are optional):
         comments (str): Can be used to put in general description or metadata related to the entire record. Can include citation links. Goes into the record's top level comments field.
@@ -311,32 +575,36 @@ class JSONGrapherRecord:
     
     Methods:
         add_data_series: Adds a new data series to the record.
-        set_layout: Updates the layout configuration for the graph.
+        add_data_series_as_equation: Adds a new equation to plot, which will be evaluated on the fly.
+        set_layout_fields: Updates the layout configuration for the graph.
         export_to_json_file: Saves the entire record (comments, datatype, data, layout) as a JSON file.
         populate_from_existing_record: Populates the attributes from an existing JSONGrapher record.
     """
-    
-    def __init__(self, comments="", graph_title="", datatype="", data_objects_list = None, simulate_as_added = True, x_data=None, y_data=None, x_axis_label_including_units="", y_axis_label_including_units ="", plot_type ="", layout={}, existing_JSONGrapher_record=None):
+
+    def __init__(self, comments="", graph_title="", datatype="", data_objects_list = None, simulate_as_added = True, evaluate_equations_as_added = True, x_data=None, y_data=None, x_axis_label_including_units="", y_axis_label_including_units ="", plot_style ="", layout=None, existing_JSONGrapher_record=None):
         """
         Initialize a JSONGrapherRecord instance with optional attributes or an existing record.
 
             layout (dict): Layout dictionary to pre-populate the graph configuration.
             existing_JSONGrapher_record (dict): Existing JSONGrapher record to populate the instance.
-        """
-        # Default attributes for a new record.
-        # Initialize the main record dictionary
-        # the if statements check if something is empty and populates them if not. This is a special syntax in python that does not require a None object to work, empty also works.
-        
-        #if receiving a data_objects_list, validate it.
+        """  
+        if layout == None: #it's bad to have an empty dictionary or list as a python argument.
+            layout = {}
+
+        # Assign self.fig_dict in a way that it will push any changes to it into the class instance.
+        self.fig_dict = {}
+
+        # If receiving a data_objects_list, validate it.
         if data_objects_list:
-            validate_plotly_data_list(data_objects_list) #call a function from outside the class.
-        #if receiving axis labels, validate them.
+            validate_plotly_data_list(data_objects_list)  # Call a function from outside the class.
+
+        # If receiving axis labels, validate them.
         if x_axis_label_including_units:
             validate_JSONGrapher_axis_label(x_axis_label_including_units, axis_name="x", remove_plural_units=False)
         if y_axis_label_including_units:
             validate_JSONGrapher_axis_label(y_axis_label_including_units, axis_name="y", remove_plural_units=False)
 
-        self.fig_dict = {
+        self.fig_dict.update( {
             "comments": comments,  # Top-level comments
             "datatype": datatype,  # Top-level datatype (datatype)
             "data": data_objects_list if data_objects_list else [],  # Data series list
@@ -344,34 +612,77 @@ class JSONGrapherRecord:
                 "title": {"text": graph_title},
                 "xaxis": {"title": {"text": x_axis_label_including_units}},
                 "yaxis": {"title": {"text": y_axis_label_including_units}}
-            }
-        }
-
+                   }
+                }
+            )
 
-        if simulate_as_added: #will try to simulate. But because this is the default, will use a try and except rather than crash program.
+        if plot_style !="":
+            self.fig_dict["plot_style"] = plot_style
+        if simulate_as_added:  # Will try to simulate, but because this is the default, will use a try-except rather than crash the program.
             try:
                 self.fig_dict = simulate_as_needed_in_fig_dict(self.fig_dict)
-            except:
-                pass
+            except KeyError:
+                pass  # Handle missing key issues gracefully
+            except Exception as e: # This is so VS code pylint does not flag this line: pylint: disable=broad-except
+                print(f"Unexpected error: {e}")  # Logs any unhandled errors
 
-        self.plot_type = plot_type #the plot_type is normally actually a series level attribute. However, if somebody sets the plot_type at the record level, then we will use that plot_type for all of the individual series.
-        if plot_type != "":
-            self.fig_dict["plot_type"] = plot_type
-
-        # Populate attributes if an existing JSONGrapher record is provided, as a dictionary.
+        if evaluate_equations_as_added:  # Will try to evaluate, but because this is the default, will use a try-except rather than crash the program.
+            try:
+                self.fig_dict = evaluate_equations_as_needed_in_fig_dict(self.fig_dict)
+            except Exception as e: # This is so VS code pylint does not flag this line. pylint: disable=broad-except, disable=unused-variable
+                pass 
+        # Populate attributes if an existing JSONGrapher record is provided as a dictionary.
         if existing_JSONGrapher_record:
             self.populate_from_existing_record(existing_JSONGrapher_record)
 
         # Initialize the hints dictionary, for use later, since the actual locations in the JSONRecord can be non-intuitive.
         self.hints_dictionary = {}
         # Adding hints. Here, the keys are the full field locations within the record.
-        self.hints_dictionary["['comments']"] = "Use Record.set_comments() to populate this field. Can be used to put in a general description or metadata related to the entire record. Can include citations and links. Goes into the record's top level comments field."
-        self.hints_dictionary["['datatype']"] = "Use Record.set_datatype() to populate this field. This is the datatype, like experiment type, and is used to assess which records can be compared and which (if any) schema to compare to. Use of single underscores between words is recommended. Avoid using double underscores '__' in this field  unless you have read the manual about hierarchical datatypes. The user can choose to provide a URL to a schema in this field, rather than a dataype name."
+        self.hints_dictionary["['comments']"] = "Use Record.set_comments() to populate this field. Can be used to put in a general description or metadata related to the entire record. Can include citations and links. Goes into the record's top-level comments field."
+        self.hints_dictionary["['datatype']"] = "Use Record.set_datatype() to populate this field. This is the datatype, like experiment type, and is used to assess which records can be compared and which (if any) schema to compare to. Use of single underscores between words is recommended. Avoid using double underscores '__' in this field unless you have read the manual about hierarchical datatypes. The user can choose to provide a URL to a schema in this field rather than a datatype name."
         self.hints_dictionary["['layout']['title']['text']"] = "Use Record.set_graph_title() to populate this field. This is the title for the graph."
-        self.hints_dictionary["['layout']['xaxis']['title']['text']"] = "Use Record.set_x_axis_label() to populate this field. This is the x axis label and should have units in parentheses. The units can include multiplication '*', division '/' and parentheses '( )'. Scientific and imperial units are recommended. Custom units can be contained in pointy brackets'< >'."  # x-axis label
-        self.hints_dictionary["['layout']['yaxis']['title']['text']"] = "Use Record.set_y_axis_label() to populate this field. This is the y axis label and should have units in parentheses. The units can include multiplication '*', division '/' and parentheses '( )'. Scientific and imperial units are recommended. Custom units can be contained in pointy brackets'< >'."
+        self.hints_dictionary["['layout']['xaxis']['title']['text']"] = "Use Record.set_x_axis_label() to populate this field. This is the x-axis label and should have units in parentheses. The units can include multiplication '*', division '/' and parentheses '( )'. Scientific and imperial units are recommended. Custom units can be contained in pointy brackets '< >'."  # x-axis label
+        self.hints_dictionary["['layout']['yaxis']['title']['text']"] = "Use Record.set_y_axis_label() to populate this field. This is the y-axis label and should have units in parentheses. The units can include multiplication '*', division '/' and parentheses '( )'. Scientific and imperial units are recommended. Custom units can be contained in pointy brackets '< >'."
+
+    ##Start of section of class code that allows class to behave like a dictionary and synchronize with fig_dict ##
+    #The __getitem__ and __setitem__ functions allow the class instance to behave 'like' a dictionary without using super.
+    #The below functions allow the JSONGrapherRecord to populate the self.fig_dict each time something is added inside.
+    #That is, if someone uses something like Record["comments"]="frog", it will also put that into self.fig_dict
+
+    def __getitem__(self, key):
+        return self.fig_dict[key]  # Direct access
+
+    def __setitem__(self, key, value):
+        self.fig_dict[key] = value  # Direct modification
+
+    def __delitem__(self, key):
+        del self.fig_dict[key]  # Support for deletion
+
+    def __iter__(self):
+        return iter(self.fig_dict)  # Allow iteration
+
+    def __len__(self):
+        return len(self.fig_dict)  # Support len()
+
+    def pop(self, key, default=None):
+        return self.fig_dict.pop(key, default)  # Implement pop()
+
+    def keys(self):
+        return self.fig_dict.keys()  # Dictionary-like keys()
+
+    def values(self):
+        return self.fig_dict.values()  # Dictionary-like values()
+
+    def items(self):
+        return self.fig_dict.items()  # Dictionary-like items()
+    
+    def update(self, *args, **kwargs):
+        """Updates the dictionary with multiple key-value pairs."""
+        self.fig_dict.update(*args, **kwargs)
 
 
+    ##End of section of class code that allows class to behave like a dictionary and synchronize with fig_dict ##
+
     #this function enables printing the current record.
     def __str__(self):
         """
@@ -381,7 +692,7 @@ class JSONGrapherRecord:
         return json.dumps(self.fig_dict, indent=4)
 
 
-    def add_data_series(self, series_name, x_values=[], y_values=[], simulate={}, simulate_as_added = True, comments="", plot_type="",  uid="", line="", extra_fields=None):
+    def add_data_series(self, series_name, x_values=None, y_values=None, simulate=None, simulate_as_added=True, comments="", trace_style="", uid="", line="", extra_fields=None):
         """
         This is the normal way of adding an x,y data series.
         """
@@ -391,10 +702,18 @@ class JSONGrapherRecord:
         # simulate: This is an optional field which, if used, is a JSON object with entries for calling external simulation scripts.
         # simulate_as_added: Boolean for calling simulation scripts immediately.
         # comments: Optional description of the data series.
-        # plot_type: Type of the data (e.g., scatter, line).
+        # trace_style: Type of the data (e.g., scatter, line, scatter_spline, spline, bar).
         # line: Dictionary describing line properties (e.g., shape, width).
         # uid: Optional unique identifier for the series (e.g., a DOI).
         # extra_fields: Dictionary containing additional fields to add to the series.
+        #Should not have mutable objects initialized as defaults, so putting them in below.
+        if x_values is None:
+            x_values = []
+        if y_values is None:
+            y_values = []
+        if simulate is None:
+            simulate = {}
+
         x_values = list(x_values)
         y_values = list(y_values)
 
@@ -406,48 +725,122 @@ class JSONGrapherRecord:
 
         #Add optional inputs.
         if len(comments) > 0:
-            data_series_dict["comments"]: comments
+            data_series_dict["comments"] = comments
         if len(uid) > 0:
-            data_series_dict["uid"]: uid
+            data_series_dict["uid"] = uid
         if len(line) > 0:
-            data_series_dict["line"]: line
+            data_series_dict["line"] = line
+        if len(trace_style) > 0:
+            data_series_dict['trace_style'] = trace_style
         #add simulate field if included.
         if simulate:
             data_series_dict["simulate"] = simulate
         if simulate_as_added: #will try to simulate. But because this is the default, will use a try and except rather than crash program.
             try:
                 data_series_dict = simulate_data_series(data_series_dict)
-            except:
+            except Exception as e: # This is so VS code pylint does not flag this line. pylint: disable=broad-except, disable=unused-variable
                 pass
         # Add extra fields if provided, they will be added.
         if extra_fields:
             data_series_dict.update(extra_fields)
-        #Add to the class object's data list.
-        self.fig_dict["data"].append(data_series_dict)
-        #update plot_type, since our internal function requires the data series to be added already.
-        if len(plot_type) > 0:
-            newest_record_index = len(self.fig_dict["data"]) - 1
-            self.set_plot_type_one_data_series(newest_record_index, plot_type)
 
+        #make this a JSONGrapherDataSeries class object, that way a person can use functions to do things like change marker size etc. more easily.
+        JSONGrapher_data_series_object = JSONGrapherDataSeries()
+        JSONGrapher_data_series_object.update_while_preserving_old_terms(data_series_dict)
+        data_series_dict = JSONGrapher_data_series_object
+        #Add to the JSONGrapherRecord class object's data list.
+        self.fig_dict["data"].append(data_series_dict) #implied return.
+        return data_series_dict
+
+    def add_data_series_as_equation(self, series_name, x_values=None, y_values=None, equation_dict=None, evaluate_equations_as_added=True, comments="", trace_style="", uid="", line="", extra_fields=None):
+        """
+        This is a way to add an equation that would be used to fill an x,y data series.
+        The equation will be a equation_dict of the json_equationer type
+        """
+        # series_name: Name of the data series.
+        # x: List of x-axis values. Or similar structure.
+        # y: List of y-axis values. Or similar structure.
+        # equation_dict: This is the field for the equation_dict of json_equationer type
+        # evaluate_equations_as_added: Boolean for evaluating equations immediately.
+        # comments: Optional description of the data series.
+        # plot_type: Type of the data (e.g., scatter, line).
+        # line: Dictionary describing line properties (e.g., shape, width).
+        # uid: Optional unique identifier for the series (e.g., a DOI).
+        # extra_fields: Dictionary containing additional fields to add to the series.
+        #Should not have mutable objects initialized as defaults, so putting them in below.
+        if x_values is None:
+            x_values = []
+        if y_values is None:
+            y_values = []
+        if equation_dict is None:
+            equation_dict = {}
+
+        x_values = list(x_values)
+        y_values = list(y_values)
+
+        data_series_dict = {
+            "name": series_name,
+            "x": x_values, 
+            "y": y_values,
+        }
+
+        #Add optional inputs.
+        if len(comments) > 0:
+            data_series_dict["comments"] = comments
+        if len(uid) > 0:
+            data_series_dict["uid"] = uid
+        if len(line) > 0:
+            data_series_dict["line"] = line
+        if len(trace_style) > 0:
+            data_series_dict['trace_style'] = trace_style
+        #add equation field if included.
+        if equation_dict:
+            data_series_dict["equation"] = equation_dict
+        # Add extra fields if provided, they will be added.
+        if extra_fields:
+            data_series_dict.update(extra_fields)
+        
+        #make this a JSONGrapherDataSeries class object, that way a person can use functions to do things like change marker size etc. more easily.
+        JSONGrapher_data_series_object = JSONGrapherDataSeries()
+        JSONGrapher_data_series_object.update_while_preserving_old_terms(data_series_dict)
+        data_series_dict = JSONGrapher_data_series_object
+        #Add to the JSONGrapherRecord class object's data list.
+        self.fig_dict["data"].append(data_series_dict)  
+        #Now evaluate the equation as added, if requested. It does seem counterintuitive to do this "at the end",
+        #but the reason this happens at the end is that the evaluation *must* occur after being a fig_dict because we
+        #need to check the units coming out against the units in the layout. Otherwise we would not be able to convert units.
+        new_data_series_index = len(self.fig_dict["data"])-1 
+        if evaluate_equations_as_added: #will try to simulate. But because this is the default, will use a try and except rather than crash program.
+            try:
+                self.fig_dict = evaluate_equation_for_data_series_by_index(self.fig_dict, new_data_series_index)
+            except Exception as e: # This is so VS code pylint does not flag this line. pylint: disable=broad-except, disable=unused-variable
+                pass
+        
     def change_data_series_name(self, series_index, series_name):
         self.fig_dict["data"][series_index]["name"] = series_name
 
     #this function forces the re-simulation of a particular dataseries.
     #The simulator link will be extracted from the record, by default.
     def simulate_data_series_by_index(self, data_series_index, simulator_link='', verbose=False):
-        data_series_dict = self.fig_dict["data"][data_series_index]
-        data_series_dict = simulate_data_series(data_series_dict, simulator_link=simulator_link, verbose=verbose)
-        self.fig_dict["data"][data_series_index] = data_series_dict #implied return
+        self.fig_dict = simulate_specific_data_series_by_index(fig_dict=self.fig_dict, data_series_index=data_series_index, simulator_link=simulator_link, verbose=verbose)
+        data_series_dict = self.fig_dict["data"][data_series_index] #implied return
         return data_series_dict #Extra regular return
-
     #this function returns the current record.
+
+    def evaluate_eqution_of_data_series_by_index(self, series_index, equation_dict = None, verbose=False):
+        if equation_dict != None:
+            self.fig_dict["data"][series_index]["equation"] = equation_dict
+        self.fig_dict = evaluate_equation_for_data_series_by_index(data_series_index=data_series_dict, verbose=verbose) #implied return.
+        return data_series_dict #Extra regular return
+
+    #this function returns the current record.       
     def get_record(self):
         """
         Returns a JSON-dict string of the record
         """
         return self.fig_dict
-
     #The update_and_validate function will clean for plotly.
+    #TODO: the internal recommending "print_to_inspect" function should, by default, exclude printing the full dictionaries of the layout_style and the trace_collection_style.
     def print_to_inspect(self, update_and_validate=True, validate=True, remove_remaining_hints=False):
         if remove_remaining_hints == True:
             self.remove_hints()
@@ -463,13 +856,14 @@ class JSONGrapherRecord:
         existing_JSONGrapher_record: A dictionary representing an existing JSONGrapher record.
         """
         #While we expect a dictionary, if a JSONGrapher ojbect is provided, we will simply pull the dictionary out of that.
-        if type(existing_JSONGrapher_record) != type({}):
-            existing_JSONGrapher_record = existing_JSONGrapher_record.fig_dict
-        if type(existing_JSONGrapher_record) == type({}):
+        if isinstance(existing_JSONGrapher_record, dict): 
             if "comments" in existing_JSONGrapher_record:   self.fig_dict["comments"] = existing_JSONGrapher_record["comments"]
             if "datatype" in existing_JSONGrapher_record:      self.fig_dict["datatype"] = existing_JSONGrapher_record["datatype"]
             if "data" in existing_JSONGrapher_record:       self.fig_dict["data"] = existing_JSONGrapher_record["data"]
             if "layout" in existing_JSONGrapher_record:     self.fig_dict["layout"] = existing_JSONGrapher_record["layout"]
+        else:
+            self.fig_dict = existing_JSONGrapher_record.fig_dict
+
 
     #the below function takes in existin JSONGrpher record, and merges the data in.
     #This requires scaling any data as needed, according to units.
@@ -512,48 +906,28 @@ class JSONGrapherRecord:
 
     #the json object can be a filename string or can be json object which is actually a dictionary.
     def import_from_json(self, json_filename_or_object):
-        if type(json_filename_or_object) == type(""): #assume it's a filename and path.
-            # Open the file in read mode with UTF-8 encoding
-            with open(json_filename_or_object, 'r', encoding='utf-8') as file:
-                # Read the entire content of the file
-                content = file.read()
-                self.fig_dict = json.loads(content)   
+        if type(json_filename_or_object) == type(""): #assume it's a json_string or filename_and_path.
+            try:
+                record = json.loads(json_filename_or_object) #first check if it's a json string.
+            except json.JSONDecodeError as e1:  # Catch specific exception
+                try:
+                    import os
+                    #if the filename does not exist, then we'll check if adding ".json" fixes the problem.
+                    if not os.path.exists(json_filename_or_object):
+                        json_added_filename = json_filename_or_object + ".json"
+                        if os.path.exists(json_added_filename): json_filename_or_object = json_added_filename #only change the filename if the json_filename exists.
+                    # Open the file in read mode with UTF-8 encoding
+                    with open(json_filename_or_object, "r", encoding="utf-8") as file:
+                        # Read the entire content of the file
+                        record = file.read().strip()  # Stripping leading/trailing whitespace
+                        self.fig_dict = json.loads(record)
+                        return self.fig_dict
+                except json.JSONDecodeError as e2:  # Catch specific exception
+                    print(f"JSON loading failed on record: {record}. Error: {e1} when trying to parse as a json directly, and {e2} when trying to use as a filename. You may want to try opening your JSON file in VS Code or in an online JSON Validator. Does your json have double quotes around strings? Single quotes around strings is allowed in python, but disallowed in JSON specifications. You may also need to check how Booleans and other aspects are defined in JSON.")  # Improved error reporting
         else:
             self.fig_dict = json_filename_or_object
+            return self.fig_dict
 
-    def set_plot_type_one_data_series(self, data_series_index, plot_type):
-        data_series_dict = self.fig_dict['data'][data_series_index]
-        data_series_dict = set_data_series_dict_plot_type(data_series_dict=data_series_dict, plot_type=plot_type)
-        #now put the data_series_dict back:
-        self.fig_dict['data'][data_series_index] = data_series_dict
-
-    def set_plot_type_all_series(self, plot_type):
-        """
-        Sets the plot_type field for the all data series.
-        options are: scatter, spline, scatter_spline
-        """
-        self.plot_type = plot_type
-        for data_series_index in range(len(self.fig_dict['data'])): #works with array indexing.
-            self.set_plot_type_one_data_series(data_series_index, plot_type)
-     
-       
-    def update_plot_types(self, plot_type=None):
-        """
-        updates the plot types for every existing data series.
-        
-        """        
-        #If optional argument not provided, take class instance setting.
-        if plot_type == None: 
-            plot_type = self.plot_type
-        #If the plot_type is not blank, use it for all series.
-        if plot_type != "":
-            self.set_plot_type_all_series(plot_type)
-        else: #if the plot_type is blank, then we will go through each data series and update them individually.
-            for data_series_index, data_series_dict in enumerate(self.fig_dict['data']):
-                #This will update the data_series_dict as needed, putting a plot_type if there is not one.
-                data_series_dict = set_data_series_dict_plot_type(data_series_dict=data_series_dict)
-                self.fig_dict['data'][data_series_index] = data_series_dict
- 
     def set_datatype(self, datatype):
         """
         Sets the datatype field used as the experiment type or schema identifier.
@@ -582,8 +956,9 @@ class JSONGrapherRecord:
         """
         if "xaxis" not in self.fig_dict['layout'] or not isinstance(self.fig_dict['layout'].get("xaxis"), dict):
             self.fig_dict['layout']["xaxis"] = {}  # Initialize x-axis as a dictionary if it doesn't exist.
-        validation_result, warnings_list, x_axis_label_including_units = validate_JSONGrapher_axis_label(x_axis_label_including_units, axis_name="x", remove_plural_units=remove_plural_units)
-        self.fig_dict['layout']["xaxis"]["title"]['text'] = x_axis_label_including_units
+        _validation_result, _warnings_list, x_axis_label_including_units = validate_JSONGrapher_axis_label(x_axis_label_including_units, axis_name="x", remove_plural_units=remove_plural_units)
+        #setdefault avoids problems for missing fields.
+        self.fig_dict.setdefault("layout", {}).setdefault("xaxis", {}).setdefault("title", {})["text"] = x_axis_label_including_units 
 
     def set_y_axis_label_including_units(self, y_axis_label_including_units, remove_plural_units=True):
         """
@@ -591,25 +966,37 @@ class JSONGrapherRecord:
         yaxis_title (str): The new title to set for the y-axis.
         """
         if "yaxis" not in self.fig_dict['layout'] or not isinstance(self.fig_dict['layout'].get("yaxis"), dict):
-            self.fig_dict['layout']["yaxis"] = {}  # Initialize y-axis as a dictionary if it doesn't exist.
-        
-        validation_result, warnings_list, y_axis_label_including_units = validate_JSONGrapher_axis_label(y_axis_label_including_units, axis_name="y", remove_plural_units=remove_plural_units)
-        self.fig_dict['layout']["yaxis"]["title"]['text'] = y_axis_label_including_units
-    
+            self.fig_dict['layout']["yaxis"] = {}  # Initialize y-axis as a dictionary if it doesn't exist.       
+        _validation_result, _warnings_list, y_axis_label_including_units = validate_JSONGrapher_axis_label(y_axis_label_including_units, axis_name="y", remove_plural_units=remove_plural_units)
+        #setdefault avoids problems for missing fields.
+        self.fig_dict.setdefault("layout", {}).setdefault("yaxis", {}).setdefault("title", {})["text"] = y_axis_label_including_units
+
+    def set_z_axis_label_including_units(self, z_axis_label_including_units, remove_plural_units=True):
+        """
+        Updates the title of the z-axis in the layout dictionary.
+        zaxis_title (str): The new title to set for the z-axis.
+        """
+        if "zaxis" not in self.fig_dict['layout'] or not isinstance(self.fig_dict['layout'].get("zaxis"), dict):
+            self.fig_dict['layout']["zaxis"] = {}  # Initialize y-axis as a dictionary if it doesn't exist.
+            self.fig_dict['layout']["zaxis"]["title"] = {}  # Initialize y-axis as a dictionary if it doesn't exist.
+        _validation_result, _warnings_list, z_axis_label_including_units = validate_JSONGrapher_axis_label(z_axis_label_including_units, axis_name="z", remove_plural_units=remove_plural_units)
+        #setdefault avoids problems for missing fields.
+        self.fig_dict.setdefault("layout", {}).setdefault("zaxis", {}).setdefault("title", {})["text"] = z_axis_label_including_units
+
     #function to set the min and max of the x axis in plotly way.
-    def set_x_axis_range(self, min, max):
-        self.fig_dict["layout"]["xaxis"][0] = min
-        self.fig_dict["layout"]["xaxis"][1] = max
+    def set_x_axis_range(self, min_value, max_value):
+        self.fig_dict["layout"]["xaxis"][0] = min_value
+        self.fig_dict["layout"]["xaxis"][1] = max_value
     #function to set the min and max of the y axis in plotly way.
-    def set_y_axis_range(self, min, max):
-        self.fig_dict["layout"]["yaxis"][0] = min
-        self.fig_dict["layout"]["yaxis"][1] = max
+    def set_y_axis_range(self, min_value, max_value):
+        self.fig_dict["layout"]["yaxis"][0] = min_value
+        self.fig_dict["layout"]["yaxis"][1] = max_value
 
     #function to scale the values in the data series by arbitrary amounts.
     def scale_record(self, num_to_scale_x_values_by = 1, num_to_scale_y_values_by = 1):
         self.fig_dict = scale_fig_dict_values(self.fig_dict, num_to_scale_x_values_by=num_to_scale_x_values_by, num_to_scale_y_values_by=num_to_scale_y_values_by)
 
-    def set_layout(self, comments="", graph_title="", x_axis_label_including_units="", y_axis_label_including_units="", x_axis_comments="",y_axis_comments="", remove_plural_units=True):
+    def set_layout_fields(self, comments="", graph_title="", x_axis_label_including_units="", y_axis_label_including_units="", x_axis_comments="",y_axis_comments="", remove_plural_units=True):
         # comments: General comments about the layout. Allowed by JSONGrapher, but will be removed if converted to a plotly object.
         # graph_title: Title of the graph.
         # xaxis_title: Title of the x-axis, including units.
@@ -617,13 +1004,12 @@ class JSONGrapherRecord:
         # yaxis_title: Title of the y-axis, including units.
         # yaxis_comments: Comments related to the y-axis.  Allowed by JSONGrapher, but will be removed if converted to a plotly object.
         
-        validation_result, warnings_list, x_axis_label_including_units = validate_JSONGrapher_axis_label(x_axis_label_including_units, axis_name="x", remove_plural_units=remove_plural_units)              
-        validation_result, warnings_list, y_axis_label_including_units = validate_JSONGrapher_axis_label(y_axis_label_including_units, axis_name="y", remove_plural_units=remove_plural_units)
+        _validation_result, _warnings_list, x_axis_label_including_units = validate_JSONGrapher_axis_label(x_axis_label_including_units, axis_name="x", remove_plural_units=remove_plural_units)              
+        _validation_result, _warnings_list, y_axis_label_including_units = validate_JSONGrapher_axis_label(y_axis_label_including_units, axis_name="y", remove_plural_units=remove_plural_units)
         self.fig_dict['layout']["title"]['text'] = graph_title
         self.fig_dict['layout']["xaxis"]["title"]['text'] = x_axis_label_including_units
         self.fig_dict['layout']["yaxis"]["title"]['text'] = y_axis_label_including_units
         
-
         #populate any optional fields, if provided:
         if len(comments) > 0:
             self.fig_dict['layout']["comments"] = comments
@@ -631,14 +1017,13 @@ class JSONGrapherRecord:
             self.fig_dict['layout']["xaxis"]["comments"] = x_axis_comments
         if len(y_axis_comments) > 0:
             self.fig_dict['layout']["yaxis"]["comments"] = y_axis_comments     
-
-
         return self.fig_dict['layout']
     
     #This function validates the output before exporting, and also has an option of removing hints.
     #The update_and_validate function will clean for plotly.
     #simulate all series will simulate any series as needed.
-    def export_to_json_file(self, filename, update_and_validate=True, validate=True, simulate_all_series = True, remove_simulate_fields= False, remove_remaining_hints=False):
+    #TODO: need to add an "include_formatting" option
+    def export_to_json_file(self, filename, update_and_validate=True, validate=True, simulate_all_series = True, remove_simulate_fields= False, remove_equation_fields= False, remove_remaining_hints=False):
         """
         writes the json to a file
         returns the json as a dictionary.
@@ -652,6 +1037,8 @@ class JSONGrapherRecord:
             self.fig_dict = simulate_as_needed_in_fig_dict(self.fig_dict)
         if remove_simulate_fields == True:
             self.fig_dict = clean_json_fig_dict(self.fig_dict, fields_to_update=['simulate'])
+        if remove_equation_fields == True:
+            self.fig_dict = clean_json_fig_dict(self.fig_dict, fields_to_update=['equation'])
         if remove_remaining_hints == True:
             self.remove_hints()
         if update_and_validate == True: #this will do some automatic 'corrections' during the validation.
@@ -670,26 +1057,66 @@ class JSONGrapherRecord:
         return self.fig_dict
 
     #simulate all series will simulate any series as needed.
-    def get_plotly_fig(self, simulate_all_series = True, update_and_validate=True):
+    def get_plotly_fig(self, plot_style=None, update_and_validate=True, simulate_all_series=True, evaluate_all_equations=True, adjust_implicit_data_ranges=True):
+        """
+        Generates a Plotly figure from the stored fig_dict, performing simulations and equations as needed.
+        By default, it will apply the default still hard coded into jsongrapher.
+
+        Args:
+            plot_style: String or dictionary of style to apply. Use '' to skip applying a style, or provide a list of length two containing both a layout style and a data series style."none" removes all style.
+            simulate_all_series (bool): If True, performs simulations for applicable series.
+            update_and_validate (bool): If True, applies automatic corrections to fig_dict.
+            evaluate_all_equations (bool): If True, evaluates all equation-based series.
+            adjust_implicit_data_ranges (bool): If True, modifies ranges for implicit data series.
+
+        Returns:
+            plotly Figure: A validated Plotly figure object based on fig_dict.
+        """
+        if plot_style is None: #should not initialize mutable objects in arguments line, so doing here.
+            plot_style = {"layout_style": "", "trace_styles_collection": ""}  # Fresh dictionary per function call
+        
         import plotly.io as pio
         import copy
-        if simulate_all_series == True:
-            self.fig_dict = simulate_as_needed_in_fig_dict(self.fig_dict)
-        original_fig_dict = copy.deepcopy(self.fig_dict) #we will get a copy, because otherwise the original fig_dict will be forced to be overwritten.
-        #if simulate_all_series is true, we'll try to simulate any series that need it, then clean the simulate fields out.
+        if plot_style == {"layout_style":"", "trace_styles_collection":""}: #if the plot_style received is the default, we'll check if the fig_dict has a plot_style.
+            plot_style = self.fig_dict.get("plot_style", {"layout_style":"", "trace_styles_collection":""}) #retrieve from self.fig_dict, and use default if not there.
+        #This code *does not* simply modify self.fig_dict. It creates a deepcopy and then puts the final x y data back in.
+        self.fig_dict = execute_implicit_data_series_operations(self.fig_dict, 
+                                                                simulate_all_series=simulate_all_series, 
+                                                                evaluate_all_equations=evaluate_all_equations, 
+                                                                adjust_implicit_data_ranges=adjust_implicit_data_ranges)
+        #Regardless of implicit data series, we make a fig_dict copy, because we will clean self.fig_dict for creating the new plotting fig object.
+        original_fig_dict = copy.deepcopy(self.fig_dict) 
+        #before cleaning and validating, we'll apply styles.
+        plot_style = parse_plot_style(plot_style=plot_style)
+        self.apply_plot_style(plot_style=plot_style)
+        #Now we clean out the fields and make a plotly object.
         if update_and_validate == True: #this will do some automatic 'corrections' during the validation.
-            self.update_and_validate_JSONGrapher_record()
-            self.fig_dict = clean_json_fig_dict(self.fig_dict, fields_to_update=['simulate', 'custom_units_chevrons'])
+            self.update_and_validate_JSONGrapher_record() #this is the line that cleans "self.fig_dict"
+            self.fig_dict = clean_json_fig_dict(self.fig_dict, fields_to_update=['simulate', 'custom_units_chevrons', 'equation', 'trace_style', '3d_axes', 'bubble'])
         fig = pio.from_json(json.dumps(self.fig_dict))
-        self.fig_dict = original_fig_dict #restore the original fig_dict.
+        #restore the original fig_dict.
+        self.fig_dict = original_fig_dict 
         return fig
 
-    #simulate all series will simulate any series as needed.
-    def plot_with_plotly(self, simulate_all_series = True, update_and_validate=True):
-        fig = self.get_plotly_fig(simulate_all_series = simulate_all_series, update_and_validate=update_and_validate)
+    #Just a wrapper aroudn plot_with_plotly.
+    def plot(self, plot_style = None, update_and_validate=True, simulate_all_series=True, evaluate_all_equations=True, adjust_implicit_data_ranges=True):
+        if plot_style is None: #should not initialize mutable objects in arguments line, so doing here.
+            plot_style = {"layout_style": "", "trace_styles_collection": ""}  # Fresh dictionary per function call
+        return self.plot_with_plotly(plot_style=plot_style, update_and_validate=update_and_validate, simulate_all_series=simulate_all_series, evaluate_all_equations=evaluate_all_equations, adjust_implicit_data_ranges=adjust_implicit_data_ranges)
+
+    #simulate all series will simulate any series as needed. If changing this function's arguments, also change those for self.plot()
+    def plot_with_plotly(self, plot_style = None, update_and_validate=True, simulate_all_series=True, evaluate_all_equations=True, adjust_implicit_data_ranges=True):
+        if plot_style is None: #should not initialize mutable objects in arguments line, so doing here.
+            plot_style = {"layout_style": "", "trace_styles_collection": ""}  # Fresh dictionary per function call
+        fig = self.get_plotly_fig(plot_style=plot_style,
+                                  simulate_all_series=simulate_all_series, 
+                                  update_and_validate=update_and_validate, 
+                                  evaluate_all_equations=evaluate_all_equations, 
+                                  adjust_implicit_data_ranges=adjust_implicit_data_ranges)
         fig.show()
         #No need for fig.close() for plotly figures.
 
+
     #simulate all series will simulate any series as needed.
     def export_to_plotly_png(self, filename, simulate_all_series = True, update_and_validate=True, timeout=10):
         fig = self.get_plotly_fig(simulate_all_series = simulate_all_series, update_and_validate=update_and_validate)       
@@ -707,7 +1134,7 @@ class JSONGrapherRecord:
         def export():
             try:
                 fig.write_image(filename, engine="kaleido")
-            except Exception as e:
+            except Exception as e: # This is so VS code pylint does not flag this line. pylint: disable=broad-except
                 print(f"Export failed: {e}")
 
         import threading
@@ -720,23 +1147,48 @@ class JSONGrapherRecord:
     #update_and_validate will 'clean' for plotly. 
     #In the case of creating a matplotlib figure, this really just means removing excess fields.
     #simulate all series will simulate any series as needed.
-    def get_matplotlib_fig(self, simulate_all_series = True, update_and_validate=True):
+    def get_matplotlib_fig(self, plot_style = None, update_and_validate=True, simulate_all_series = True, evaluate_all_equations = True, adjust_implicit_data_ranges=True):
+        """
+        Generates a matplotlib figure from the stored fig_dict, performing simulations and equations as needed.
+
+        Args:
+            simulate_all_series (bool): If True, performs simulations for applicable series.
+            update_and_validate (bool): If True, applies automatic corrections to fig_dict.
+            evaluate_all_equations (bool): If True, evaluates all equation-based series.
+            adjust_implicit_data_ranges (bool): If True, modifies ranges for implicit data series.
+
+        Returns:
+            plotly Figure: A validated matplotlib figure object based on fig_dict.
+        """
+        if plot_style is None: #should not initialize mutable objects in arguments line, so doing here.
+            plot_style = {"layout_style": "", "trace_styles_collection": ""}  # Fresh dictionary per function call
         import copy
-        #if simulate_all_series is true, we'll try to simulate any series that need it, then clean the simulate fields out.
-        if simulate_all_series == True:
-            self.fig_dict = simulate_as_needed_in_fig_dict(self.fig_dict)
+        if plot_style == {"layout_style":"", "trace_styles_collection":""}: #if the plot_style received is the default, we'll check if the fig_dict has a plot_style.
+            plot_style = self.fig_dict.get("plot_style", {"layout_style":"", "trace_styles_collection":""})
+        #This code *does not* simply modify self.fig_dict. It creates a deepcopy and then puts the final x y data back in.
+        self.fig_dict = execute_implicit_data_series_operations(self.fig_dict, 
+                                                                simulate_all_series=simulate_all_series, 
+                                                                evaluate_all_equations=evaluate_all_equations, 
+                                                                adjust_implicit_data_ranges=adjust_implicit_data_ranges)
+        #Regardless of implicit data series, we make a fig_dict copy, because we will clean self.fig_dict for creating the new plotting fig object.
         original_fig_dict = copy.deepcopy(self.fig_dict) #we will get a copy, because otherwise the original fig_dict will be forced to be overwritten.    
+        #before cleaning and validating, we'll apply styles.
+        plot_style = parse_plot_style(plot_style=plot_style)
+        self.apply_plot_style(plot_style=plot_style)
         if update_and_validate == True: #this will do some automatic 'corrections' during the validation.
             self.update_and_validate_JSONGrapher_record()
-            self.fig_dict = clean_json_fig_dict(self.fig_dict, fields_to_update=['simulate', 'custom_units_chevrons'])
+            self.fig_dict = clean_json_fig_dict(self.fig_dict, fields_to_update=['simulate', 'custom_units_chevrons', 'equation', 'trace_style'])
         fig = convert_JSONGrapher_dict_to_matplotlib_fig(self.fig_dict)
         self.fig_dict = original_fig_dict #restore the original fig_dict.
         return fig
 
     #simulate all series will simulate any series as needed.
-    def plot_with_matplotlib(self, simulate_all_series = True, update_and_validate=True):
+    def plot_with_matplotlib(self, update_and_validate=True, simulate_all_series=True, evaluate_all_equations=True, adjust_implicit_data_ranges=True):
         import matplotlib.pyplot as plt
-        fig = self.get_matplotlib_fig(simulate_all_series = simulate_all_series, update_and_validate=update_and_validate)
+        fig = self.get_matplotlib_fig(simulate_all_series=simulate_all_series, 
+                                      update_and_validate=update_and_validate, 
+                                      evaluate_all_equations=evaluate_all_equations, 
+                                      adjust_implicit_data_ranges=adjust_implicit_data_ranges)
         plt.show()
         plt.close(fig) #remove fig from memory.
 
@@ -811,9 +1263,130 @@ class JSONGrapherRecord:
                     if current_field.get(current_path_key, "") == hint_text:
                         current_field[current_path_key] = ""
 
+    ## Start of section of JSONGRapher class functions related to styles ##
+
+    def apply_plot_style(self, plot_style= None): 
+        #the plot_style can be a string, or a plot_style dictionary {"layout_style":"default", "trace_styles_collection":"default"} or a list of length two with those two items.
+        #The plot_style dictionary can include a pair of dictionaries.
+        #if apply style is called directly, we will first put the plot_style into the plot_style field
+        #This way, the style will stay.
+        if plot_style is None: #should not initialize mutable objects in arguments line, so doing here.
+            plot_style = {"layout_style": "", "trace_styles_collection": ""}  # Fresh dictionary per function call
+        self.fig_dict['plot_style'] = plot_style
+        self.fig_dict = apply_plot_style_to_plotly_dict(self.fig_dict, plot_style=plot_style)
+    def remove_plot_style(self):
+        self.fig_dict.pop("plot_style") #This line removes the field of plot_style from the fig_dict.
+        self.fig_dict = remove_plot_style_from_plotly_dict(self.fig_dict) #This line removes the actual formatting from the fig_dict.
+    def set_layout_style(self, layout_style):
+        if "plot_style" not in self.fig_dict: #create it not present.
+            self.fig_dict["plot_style"] = {}  # Initialize if missing
+        self.fig_dict["plot_style"]["layout_style"] = layout_style
+    def remove_layout_style_setting(self):
+        if "layout_style" in self.fig_dict["plot_style"]:
+            self.fig_dict["plot_style"].pop("layout_style")
+    def extract_layout_style(self):
+        layout_style = extract_layout_style_from_plotly_dict(self.fig_dict)
+        return layout_style
+    def apply_trace_style_by_index(self, data_series_index, trace_styles_collection='', trace_style=''):
+        if trace_styles_collection == '':
+            self.fig_dict.setdefault("plot_style",{}) #create the plot_style dictionary if it's not there. Else, return current value.
+            trace_styles_collection = self.fig_dict["plot_style"].get("trace_styles_collection", '') #check if there is a trace_styles_collection within it, and use that. If it's not there, then use ''.
+        #trace_style should be a dictionary, but can be a string.
+        data_series = self.fig_dict["data"][data_series_index]
+        data_series = apply_trace_style_to_single_data_series(data_series, trace_styles_collection=trace_styles_collection, trace_style_to_apply=trace_style) #this is the 'external' function, not the one in the class.
+        self.fig_dict["data"][data_series_index] = data_series
+        return data_series
+    def set_trace_style_one_data_series(self, data_series_index, trace_style):
+        self.fig_dict['data'][data_series_index]["trace_style"] = trace_style
+        return self.fig_dict['data'][data_series_index]
+    def set_trace_styles_collection(self, trace_styles_collection):
+        """
+        Sets the plot_style["trace_styles_collection"] field for the all data series.
+        options are: scatter, spline, scatter_spline
+        """
+        self.fig_dict["plot_style"]["trace_styles_collection"] = trace_styles_collection
+    def remove_trace_styles_collection_setting(self):
+        if "trace_styles_collection" in self.fig_dict["plot_style"]:
+            self.fig_dict["plot_style"].pop("trace_styles_collection")
+    def set_trace_style_all_series(self, trace_style):
+        """
+        Sets the trace_style field for the all data series.
+        options are: scatter, spline, scatter_spline
+        """
+        for data_series_index in range(len(self.fig_dict['data'])): #works with array indexing.
+            self.set_trace_style_one_data_series(data_series_index, trace_style)
+    def extract_trace_styles_collection(self, new_trace_styles_collection_name='', 
+                                    indices_of_data_series_to_extract_styles_from=None, 
+                                    new_trace_style_names_list=None, extract_colors=False):
+        """
+        Extracts trace style collection 
+        :param new_trace_styles_collection_name: str, Name of the new collection.
+        :param indices_of_data_series_to_extract_styles_from: list, Indices of series to extract styles from.
+        :param new_trace_style_names_list: list, Names for the new trace styles.
+        """
+        if indices_of_data_series_to_extract_styles_from is None:  # should not initialize mutable objects in arguments line, so doing here.
+            indices_of_data_series_to_extract_styles_from = []  
+        if new_trace_style_names_list is None:  # should not initialize mutable objects in arguments line, so doing here.
+            new_trace_style_names_list = []
+        fig_dict = self.fig_dict
+        new_trace_styles_collection_dictionary_without_name = {}
+        if new_trace_styles_collection_name == '':
+            new_trace_styles_collection_name = 'replace_this_with_your_trace_styles_collection_name'
+        if indices_of_data_series_to_extract_styles_from == []:
+            indices_of_data_series_to_extract_styles_from = range(len(fig_dict["data"]))
+        if new_trace_style_names_list == []:
+            for data_series_index in indices_of_data_series_to_extract_styles_from:
+                data_series_dict = fig_dict["data"][data_series_index]
+                trace_style_name = data_series_dict.get('trace_style', '')  # return blank line if not there.
+                if trace_style_name == '':
+                    trace_style_name = 'custom_trace_style' + str(data_series_index)
+                if trace_style_name not in new_trace_style_names_list:
+                    pass
+                else:
+                    trace_style_name = trace_style_name + str(data_series_index)
+                new_trace_style_names_list.append(trace_style_name)
+        if len(indices_of_data_series_to_extract_styles_from) != len(new_trace_style_names_list):
+            raise ValueError("Error: The input for indices_of_data_series_to_extract_styles_from is not compatible with the input for new_trace_style_names_list. There is a difference in lengths after the automatic parsing and filling that occurs.")
+        for index_to_extract_from in indices_of_data_series_to_extract_styles_from:
+            new_trace_style_name = new_trace_style_names_list[index_to_extract_from]
+            extracted_trace_style = extract_trace_style_by_index(fig_dict, index_to_extract_from, new_trace_style_name=new_trace_style_names_list[index_to_extract_from], extract_colors=extract_colors)
+            new_trace_styles_collection_dictionary_without_name[new_trace_style_name] = extracted_trace_style[new_trace_style_name]
+        return new_trace_styles_collection_name, new_trace_styles_collection_dictionary_without_name
+    def export_trace_styles_collection(self, new_trace_styles_collection_name='', 
+                                    indices_of_data_series_to_extract_styles_from=None, 
+                                    new_trace_style_names_list=None, filename='', extract_colors=False):
+        """
+        Exports trace style collection while ensuring proper handling of mutable default arguments.
+        
+        :param new_trace_styles_collection_name: str, Name of the new collection.
+        :param indices_of_data_series_to_extract_styles_from: list, Indices of series to extract styles from.
+        :param new_trace_style_names_list: list, Names for the new trace styles.
+        :param filename: str, Name of the file to export to.
+        """
+        if indices_of_data_series_to_extract_styles_from is None:  # should not initialize mutable objects in arguments line, so doing here.
+            indices_of_data_series_to_extract_styles_from = []
+        if new_trace_style_names_list is None:  # should not initialize mutable objects in arguments line, so doing here.
+            new_trace_style_names_list = []
+        auto_new_trace_styles_collection_name, new_trace_styles_collection_dictionary_without_name = self.extract_trace_styles_collection(new_trace_styles_collection_name=new_trace_styles_collection_name, indices_of_data_series_to_extract_styles_from=indices_of_data_series_to_extract_styles_from, new_trace_style_names_list = new_trace_style_names_list, extract_colors=extract_colors)
+        if new_trace_styles_collection_name == '':
+            new_trace_styles_collection_name = auto_new_trace_styles_collection_name
+        if filename == '':
+            filename = new_trace_styles_collection_name
+        write_trace_styles_collection_to_file(trace_styles_collection=new_trace_styles_collection_dictionary_without_name, trace_styles_collection_name=new_trace_styles_collection_name, filename=filename)
+        return new_trace_styles_collection_name, new_trace_styles_collection_dictionary_without_name
+    def extract_trace_style_by_index(self, data_series_index, new_trace_style_name='', extract_colors=False):
+        extracted_trace_style = extract_trace_style_by_index(self.fig_dict, data_series_index, new_trace_style_name=new_trace_style_name, extract_colors=extract_colors)
+        return extracted_trace_style
+    def export_trace_style_by_index(self, data_series_index, new_trace_style_name='', filename='', extract_colors=False):
+        extracted_trace_style = extract_trace_style_by_index(self.fig_dict, data_series_index, new_trace_style_name=new_trace_style_name, extract_colors=extract_colors)
+        new_trace_style_name = list(extracted_trace_style.keys())[0] #the extracted_trace_style will have a single key which is the style name.
+        if filename == '': 
+            filename = new_trace_style_name
+        write_trace_style_to_file(trace_style_dict=extracted_trace_style[new_trace_style_name],trace_style_name=new_trace_style_name, filename=filename)
+        return extracted_trace_style       
+    ## End of section of JSONGRapher class functions related to styles ##
+
     #Make some pointers to external functions, for convenience, so people can use syntax like record.function_name() if desired.
-    def apply_style(self, style_name):
-        self.fig_dict = apply_style_to_plotly_dict(self.fig_dict, style_name=style_name)
     def validate_JSONGrapher_record(self):
         validate_JSONGrapher_record(self)
     def update_and_validate_JSONGrapher_record(self):
@@ -877,16 +1450,16 @@ def units_plural_removal(units_to_check):
               - "changed" (Boolean): True, or False, where True means the string was changed to remove an "s" at the end.
               - "singularized" (string): The units parsed to be singular, if needed.
     """
-    #Check if we have the module we need. If not, return with no change.
+    # Check if we have the module we need. If not, return with no change.
     try:
         import JSONGrapher.units_list as units_list
-    except:
-        #if JSONGrapher is not present, try getting the units_list file locally.
+    except ImportError:
         try:
-            import units_list
-        except:#if still not present, give up and avoid crashing.
+            from . import units_list  # Attempt local import
+        except ImportError as exc:  # If still not present, give up and avoid crashing
             units_changed_flag = False
-            return units_changed_flag, units_to_check #return None if there was no test.
+            print(f"Module import failed: {exc}")  # Log the error for debugging
+            return units_changed_flag, units_to_check  # Return unchanged values
 
     #First try to check if units are blank or ends with "s" is in the units list. 
     if (units_to_check == "") or (units_to_check[-1] != "s"):
@@ -904,41 +1477,51 @@ def units_plural_removal(units_to_check):
             else: #No change if the truncated string isn't found.
                 units_changed_flag = False
                 units_singularized = units_to_check
+    else:
+        units_changed_flag = False
+        units_singularized = units_to_check  #if it's outside of ourknown logic, we just return unchanged.
     return units_changed_flag, units_singularized
 
 
 def separate_label_text_from_units(label_with_units):
-    """
-    Parses a label with text string and units in parentheses after that to return the two parts.
-    This is not meant to separate strings like "Time (s)", it is not meant for strings like "5 (kg)"
+    # Check for mismatched parentheses
+    open_parentheses = label_with_units.count('(')
+    close_parentheses = label_with_units.count(')')
+    
+    if open_parentheses != close_parentheses:
+        raise ValueError(f"Mismatched parentheses in input string: '{label_with_units}'")
 
-    Args:
-        value (str): A string containing a label and optional units enclosed in parentheses.
-                     Example: "Time (Years)" or "Speed (km/s)
+    # Default parsed output
+    parsed_output = {"text": label_with_units, "units": ""}
 
-    Returns:
-        dict: A dictionary with two keys:
-              - "text" (str): The label text parsed from the input string.
-              - "units" (str): The units parsed from the input string, or an empty string if no units are present.
-    """
-    # Find the position of the first '(' and the last ')'
+    # Extract tentative start and end indices, from first open and first close parentheses.
     start = label_with_units.find('(')
     end = label_with_units.rfind(')')
-    
-    # Ensure both are found and properly ordered
-    if start != -1 and end != -1 and end > start:
-        text_part = label_with_units[:start].strip()  # Everything before '('
-        units_part = label_with_units[start + 1:end].strip()  # Everything inside '()'
+
+    # Flag to track if the second check fails
+    second_check_failed = False
+
+    # Ensure removing both first '(' and last ')' doesn't cause misalignment
+    if start != -1 and end != -1:
+        temp_string = label_with_units[:start] + label_with_units[start + 1:end] + label_with_units[end + 1:]  # Removing first '(' and last ')'
+        first_closing_paren_after_removal = temp_string.find(')')
+        first_opening_paren_after_removal = temp_string.find('(')
+        if first_opening_paren_after_removal != -1 and first_closing_paren_after_removal < first_opening_paren_after_removal:
+            second_check_failed = True  # Set flag if second check fails
+
+    if second_check_failed:
+        #For the units, keep everything from the first '(' onward
+        parsed_output["text"] = label_with_units[:start].strip()
+        parsed_output["units"] = label_with_units[start:].strip()
     else:
-        text_part = label_with_units
-        units_part = ""
-    parsed_output = {
-                "text":text_part,
-                "units":units_part
-            }
+        # Extract everything between first '(' and last ')'
+        parsed_output["text"] = label_with_units[:start].strip()
+        parsed_output["units"] = label_with_units[start + 1:end].strip()
+
     return parsed_output
 
 
+
 def validate_plotly_data_list(data):
     """
     Validates the entries in a Plotly data array.
@@ -973,29 +1556,29 @@ def validate_plotly_data_list(data):
         if "comments" in trace:
             warnings_list.append(f"Trace {i} has a comments field within the data. This is allowed by JSONGrapher, but is discouraged by plotly. By default, this will be removed when you export your record.")
         # Determine the type based on the fields provided
-        trace_type = trace.get("type")
-        if not trace_type:
+        trace_style = trace.get("type")
+        if not trace_style:
             # Infer type based on fields and attributes
             if "x" in trace and "y" in trace:
                 if "mode" in trace or "marker" in trace or "line" in trace:
-                    trace_type = "scatter"
+                    trace_style = "scatter"
                 elif "text" in trace or "marker.color" in trace:
-                    trace_type = "bar"
+                    trace_style = "bar"
                 else:
-                    trace_type = "scatter"  # Default assumption
+                    trace_style = "scatter"  # Default assumption
             elif "labels" in trace and "values" in trace:
-                trace_type = "pie"
+                trace_style = "pie"
             elif "z" in trace:
-                trace_type = "heatmap"
+                trace_style = "heatmap"
             else:
                 warnings_list.append(f"Trace {i} cannot be inferred as a valid type.")
                 continue
         
         # Check for required fields
-        required_fields = required_fields_by_type.get(trace_type, [])
+        required_fields = required_fields_by_type.get(trace_style, [])
         for field in required_fields:
             if field not in trace:
-                warnings_list.append(f"Trace {i} (type inferred as {trace_type}) is missing required field: {field}.")
+                warnings_list.append(f"Trace {i} (type inferred as {trace_style}) is missing required field: {field}.")
 
     if warnings_list:
         print("Warning: There are some entries in your data list that did not pass validation checks: \n", warnings_list)
@@ -1021,7 +1604,6 @@ def parse_units(value):
     # Find the position of the first '(' and the last ')'
     start = value.find('(')
     end = value.rfind(')')
-    print("line 727", value)
     # Ensure both are found and properly ordered
     if start != -1 and end != -1 and end > start:
         number_part = value[:start].strip()  # Everything before '('
@@ -1038,75 +1620,9 @@ def parse_units(value):
     
     return parsed_output
 
-
-#This function sets the plot_type of a data_series_dict
-#based on some JSONGrapher options.
-#It calls "plot_type_to_field_values" 
-#and then updates the data_series_dict accordingly, as needed.
-def set_data_series_dict_plot_type(data_series_dict, plot_type=""):
-    if plot_type == "":
-        plot_type = data_series_dict.get('type', 'scatter') #get will return the second argument if the first argument is not present.       
-    #We need to be careful about one case: in plotly, a "spline" is declared a scatter plot with data.line.shape = spline. 
-    #So we need to check if we have spline set, in which case we make the plot_type scatter_spline when calling plot_type_to_field_values.
-    shape_field = data_series_dict.get('line', {}).get('shape', '') #get will return first argument if there, second if not, so can chain things.
-    #TODO: need to distinguish between "spline" and "scatter_spline" by checking for marker instructions.
-    if shape_field == 'spline':
-        plot_type = 'scatter_spline' 
-    if shape_field == 'linear':
-        plot_type = 'scatter_line' 
-    fields_dict = plot_type_to_field_values(plot_type)
- 
-    
-    #update the data_series_dict.
-    if fields_dict.get("mode_field"):
-        data_series_dict["mode"] = fields_dict["mode_field"]
-    if fields_dict.get("type_field"):
-        data_series_dict["type"] = fields_dict["type_field"]
-    if fields_dict.get("line_shape_field") != "":
-        data_series_dict.setdefault("line", {"shape": ''})  # Creates the field if it does not already exist.
-        data_series_dict["line"]["shape"] = fields_dict["line_shape_field"]
-    return data_series_dict
-
-#This function creates a fields_dict for the function set_data_series_dict_plot_type
-def plot_type_to_field_values(plot_type):
-    """
-    Takes in a string that is a plot type, such as "scatter", "scatter_spline", etc.
-    and returns the field values that would have to go into a plotly data object.
-
-    Returns:
-        dict: A dictionary with keys and values for the fields that will be ultimately filled.
-
-    To these fields are used in the function set_plot_type_one_data_series
-
-    """
-    fields_dict = {}
-    #initialize some variables.
-    fields_dict["type_field"] = plot_type.lower()
-    fields_dict["mode_field"] = None
-    fields_dict["line_shape_field"] = None
-    # Assign the various types. This list of values was determined 'manually'.
-    if plot_type.lower() == ("scatter" or "markers"):
-        fields_dict["type_field"] = "scatter"
-        fields_dict["mode_field"] = "markers"
-        fields_dict["line_shape_field"] = None
-    elif plot_type.lower() == "scatter_spline":
-        fields_dict["type_field"] = "scatter"
-        fields_dict["mode_field"] = None
-        fields_dict["line_shape_field"] = "spline"
-    elif plot_type.lower() == "spline":
-        fields_dict["type_field"] = 'scatter'
-        fields_dict["mode_field"] = 'lines'
-        fields_dict["line_shape_field"] = "spline"
-    elif plot_type.lower() == "scatter_line":
-        fields_dict["type_field"] = 'scatter'
-        fields_dict["mode_field"] = 'lines'
-        fields_dict["line_shape_field"] = "linear"
-    return fields_dict
-
 #This function does updating of internal things before validating
 #This is used before printing and returning the JSON record.
 def update_and_validate_JSONGrapher_record(record, clean_for_plotly=True):
-    record.update_plot_types()
     record.validate_JSONGrapher_record()
     if clean_for_plotly == True:
         record.fig_dict = clean_json_fig_dict(record.fig_dict)
@@ -1202,41 +1718,150 @@ def validate_JSONGrapher_record(record):
     else:
         return True, []
 
-def rolling_polynomial_fit(x_values, y_values, window_size=3, degree=2):
+def rolling_polynomial_fit(x_values, y_values, window_size=3, degree=2, num_interpolated_points=0, adjust_edges=True):
     """
-    Applies a rolling polynomial regression with a specified window size and degree.
+    Applies a rolling polynomial regression with a specified window size and degree,
+    interpolates additional points, and optionally adjusts edge points for smoother transitions.
 
     Args:
         x_values (list): List of x coordinates.
         y_values (list): List of y coordinates.
         window_size (int): Number of points per rolling fit (default: 3).
         degree (int): Degree of polynomial to fit (default: 2).
+        num_interpolated_points (int): Number of interpolated points per segment (default: 3). Set to 0 to only return original points.
+        adjust_edges (bool): Whether to adjust edge cases based on window size (default: True).
 
     Returns:
         tuple: (smoothed_x, smoothed_y) lists for plotting.
     """
     import numpy as np
+
     smoothed_y = []
-    smoothed_x = x_values  # Keep x values unchanged
+    smoothed_x = []
 
     half_window = window_size // 2  # Number of points to take before & after
 
-    for i in range(len(y_values)):
-        # Handle edge cases: First and last points have fewer neighbors
+    for i in range(len(y_values) - 1):
+        # Handle edge cases dynamically based on window size
         left_bound = max(0, i - half_window)
         right_bound = min(len(y_values), i + half_window + 1)
 
+        if adjust_edges:
+            if i == 0:  # First point
+                right_bound = min(len(y_values), i + window_size)  # Expand to use more points near start
+            elif i == len(y_values) - 2:  # Last point
+                left_bound = max(0, i - (window_size - 1))  # Expand to include more points near end
+
         # Select the windowed data
         x_window = np.array(x_values[left_bound:right_bound])
         y_window = np.array(y_values[left_bound:right_bound])
 
+        # Adjust degree based on window size
+        adjusted_degree = degree if len(x_window) > 2 else 1  # Use linear fit if only two points are available
+
         # Fit polynomial & evaluate at current point
-        poly_coeffs = np.polyfit(x_window, y_window, deg=degree)
-        smoothed_y.append(np.polyval(poly_coeffs, x_values[i]))
+        poly_coeffs = np.polyfit(x_window, y_window, deg=adjusted_degree)
+
+        # Generate interpolated points between x_values[i] and x_values[i+1]
+        x_interp = np.linspace(x_values[i], x_values[i+1], num_interpolated_points + 2)  # Including endpoints
+        y_interp = np.polyval(poly_coeffs, x_interp)
+
+        smoothed_x.extend(x_interp)
+        smoothed_y.extend(y_interp)
 
     return smoothed_x, smoothed_y
 
 
+
+## Start of Section of Code for Styles and Converting between plotly and matplotlib Fig objectss ##
+# #There are a few things to know about the styles logic of JSONGrapher:
+# (1) There are actually two parts to the plot_style: a layout_style for the graph and a trace_styles_collection which will get applied to the individual dataseries.
+#    So the plot_style is really supposed to be a dictionary with {"layout_style":"default", "trace_styles_collection":"default"} that way it is JSON compatible and avoids ambiguity. 
+#    A person can pass in dictionaries for layout_style and for trace_styles_collection and thereby create custom styles.
+#    There are helper functions to extract style dictionaries once a person has a JSONGrapher record which they're happy with.
+# (2) We parse what the person provides as a style, so we accept things other than the ideal plot_style dictionary format.  
+#    If someone provides a single string, we'll use it for both layout_style and trace_styles_collection.
+#    If we get a list of two, we'll expect that to be in the order of layout_style then trace_styles_collection
+#    If we get a string that we can't find in the existing styles list, then we'll use the default. 
+# (1) by default, exporting a JSONGRapher record to file will *not* include plot_styles.  include_formatting will be an optional argument. 
+# (2) There is an apply_plot_style function which will first put the style into self.fig_dict['plot_style'] so it stays there, before applying the style.
+# (3) For the plotting functions, they will have plot_style = {"layout_style":"", "trace_styles_collection":""} or = '' as their default argument value, which will result in checking if plot_style exists in the self.fig_dict already. If so, it will be used. 
+#     If somebody passes in a "None" type or the word none, then *no* style changes will be applied during plotting, relative to what the record already has.
+#     One can pass a style in for the plotting functions. In those cases, we'll use the remove style option, then apply.
+
+def parse_plot_style(plot_style):
+    """
+    Parse the given plot style and return a structured dictionary for layout and data series styles.
+    If plot_style is missing a layout_style or trace_styles_collection then will set them as an empty string.
+    
+    :param plot_style: None, str, list of two items, or a dictionary with at least one valid field.
+    :return: dict with "layout_style" and "trace_styles_collection", ensuring defaults if missing.
+    """
+    if plot_style is None:
+        parsed_plot_style = {"layout_style": None, "trace_styles_collection": None}
+    elif isinstance(plot_style, str):
+        parsed_plot_style = {"layout_style": plot_style, "trace_styles_collection": plot_style}
+    elif isinstance(plot_style, list) and len(plot_style) == 2:
+        parsed_plot_style = {"layout_style": plot_style[0], "trace_styles_collection": plot_style[1]}
+    elif isinstance(plot_style, dict):
+        if "trace_styles_collection" not in plot_style:
+            if "trace_style_collection" in plot_style:
+                print("Warning: plot_style has 'trace_style_collection', this key should be 'trace_styles_collection'.  The key is being used, but the spelling error should be fixed.")
+                plot_style["traces_styles_collection"] = plot_style["trace_style_collection"]
+            elif "traces_style_collection" in plot_style:
+                print("Warning: plot_style has 'traces_style_collection', this key should be 'trace_styles_collection'.  The key is being used, but the spelling error should be fixed.")
+                plot_style["traces_styles_collection"] = plot_style["traces_style_collection"]
+            else:
+                plot_style.setdefault("trace_styles_collection", '')
+        if "layout_style" not in plot_style: 
+            plot_style.setdefault("layout_style", '')
+        parsed_plot_style = {
+            "layout_style": plot_style.get("layout_style", None),
+            "trace_styles_collection": plot_style.get("trace_styles_collection", None),
+        }
+    else:
+        raise ValueError("Invalid plot style: Must be None, a string, a list of two items, or a dictionary with valid fields.")
+    return parsed_plot_style
+
+#this function uses a stylename or list of stylename/dictionaries to apply *both* layout_style and trace_styles_collection
+#plot_style is a dictionary of form {"layout_style":"default", "trace_styles_collection":"default"}
+#However, the style_to_apply does not need to be passed in as a dictionary.
+#For example: style_to_apply = ['default', 'default'] or style_to_apply = 'science'.
+#IMPORTANT: This is the only function that will set a layout_style or trace_styles_collection that is an empty string into 'default'.
+# all other style applying functions (including parse_plot_style) will pass on the empty string or will do nothing if receiving an empty string.
+def apply_plot_style_to_plotly_dict(fig_dict, plot_style=None):
+    if plot_style is None:  # should not initialize mutable objects in arguments line, so doing here.
+        plot_style = {"layout_style": {}, "trace_styles_collection": {}}  # Fresh dictionary per function call
+    #We first parse style_to_apply to get a properly formatted plot_style dictionary of form: {"layout_style":"default", "trace_styles_collection":"default"}
+    plot_style = parse_plot_style(plot_style)
+    plot_style.setdefault("layout_style",'') #fill with blank string if not present.
+    plot_style.setdefault("trace_styles_collection",'')  #fill with blank string if not present.
+    #Code logic for layout style.
+    if str(plot_style["layout_style"]).lower() != 'none': #take no action if received "None" or NoneType
+        if plot_style["layout_style"] == '': #in this case, we're going to use the default.
+            plot_style["layout_style"] = 'default'
+        fig_dict = remove_layout_style_from_plotly_dict(fig_dict=fig_dict)
+        fig_dict = apply_layout_style_to_plotly_dict(fig_dict=fig_dict, layout_style_to_apply=plot_style["layout_style"])
+    #Code logic for trace_styles_collection style.
+    if str(plot_style["trace_styles_collection"]).lower() != 'none': #take no action if received "None" or NoneType
+        if plot_style["trace_styles_collection"] == '': #in this case, we're going to use the default.
+            plot_style["trace_styles_collection"] = 'default'            
+        fig_dict = remove_trace_styles_collection_from_plotly_dict(fig_dict=fig_dict)
+        fig_dict = apply_trace_styles_collection_to_plotly_dict(fig_dict=fig_dict,trace_styles_collection=plot_style["trace_styles_collection"])
+    return fig_dict
+
+def remove_plot_style_from_plotly_dict(fig_dict):
+    """
+    Remove both layout and data series styles from a Plotly figure dictionary.
+
+    :param fig_dict: dict, Plotly style fig_dict
+    :return: dict, Updated Plotly style fig_dict with default formatting.
+    """
+    fig_dict = remove_layout_style_from_plotly_dict(fig_dict)
+    fig_dict = remove_trace_styles_collection_from_plotly_dict(fig_dict)
+    return fig_dict
+
+
 def convert_JSONGrapher_dict_to_matplotlib_fig(fig_dict):
     """
     Converts a Plotly figure dictionary into a Matplotlib figure without using pio.from_json.
@@ -1251,30 +1876,40 @@ def convert_JSONGrapher_dict_to_matplotlib_fig(fig_dict):
     fig, ax = plt.subplots()
 
     # Extract traces (data series)
+    #This section is now deprecated. It has not been completely updated after the trace_style field was created.
+    #There was old logic for plotly_trace_type which has been partially updated, but in fact the logic should be rewritten
+    #to better accommodate the existence of both "trace_style" and "type". It may be that there should be
+    #a helper function called 
     for trace in fig_dict.get("data", []):
-        trace_type = trace.get("type", None)
+        trace_style = trace.get("trace_style", '')
+        plotly_trace_types = trace.get("type", '')
+        if (plotly_trace_types == '') and (trace_style == ''):
+            trace_style = 'scatter_spline'
+        elif (plotly_trace_types == 'scatter') and (trace_style == ''):
+            trace_style = 'scatter_spline'
+        elif (trace_style == '') and (plotly_trace_types != ''):
+            trace_style = plotly_trace_types
         # If type is missing, but mode indicates lines and shape is spline, assume it's a spline
-        if not trace_type and trace.get("mode") == "lines" and trace.get("line", {}).get("shape") == "spline":
-            trace_type = "spline"
-
+        if not trace_style and trace.get("mode") == "lines" and trace.get("line", {}).get("shape") == "spline":
+            trace_style = "spline"
         x_values = trace.get("x", [])
         y_values = trace.get("y", [])
         trace_name = trace.get("name", "Data")
-        if trace_type == "bar":
+        if trace_style == "bar":
             ax.bar(x_values, y_values, label=trace_name)
-
-        elif trace_type == "scatter":
+        elif trace_style == "scatter":
+            mode = trace.get("mode", "")
+            ax.scatter(x_values, y_values, label=trace_name, alpha=0.7)
+        elif trace_style == "scatter_spline":
             mode = trace.get("mode", "")
             ax.scatter(x_values, y_values, label=trace_name, alpha=0.7)
-
             # Attempt to simulate spline behavior if requested
             if "lines" in mode or trace.get("line", {}).get("shape") == "spline":
                 print("Warning: Rolling polynomial approximation used instead of spline.")
                 x_smooth, y_smooth = rolling_polynomial_fit(x_values, y_values, window_size=3, degree=2)
-                
                 # Add a label explicitly for the legend
                 ax.plot(x_smooth, y_smooth, linestyle="-", label=f"{trace_name} Spline")
-        elif trace_type == "spline":
+        elif trace_style == "spline":
             print("Warning: Using rolling polynomial approximation instead of true spline.")
             x_smooth, y_smooth = rolling_polynomial_fit(x_values, y_values, window_size=3, degree=2)
             ax.plot(x_smooth, y_smooth, linestyle="-", label=f"{trace_name} Spline")
@@ -1307,9 +1942,6 @@ def convert_JSONGrapher_dict_to_matplotlib_fig(fig_dict):
     return fig
     
 
-
-
-
 #The below function works, but because it depends on the python plotly package, we avoid using it
 #To decrease the number of dependencies. 
 def convert_plotly_dict_to_matplotlib(fig_dict):
@@ -1327,7 +1959,7 @@ def convert_plotly_dict_to_matplotlib(fig_dict):
         matplotlib.figure.Figure: The corresponding Matplotlib figure.
     """
     import plotly.io as pio
-
+    import matplotlib.pyplot as plt
     # Convert JSON dictionary into a Plotly figure
     plotly_fig = pio.from_json(json.dumps(fig_dict))
 
@@ -1357,97 +1989,1045 @@ def convert_plotly_dict_to_matplotlib(fig_dict):
     ax.set_ylabel(plotly_fig.layout.yaxis.title.text if plotly_fig.layout.yaxis.title else "Y-Axis")
 
     return fig
+
+def apply_trace_styles_collection_to_plotly_dict(fig_dict, trace_styles_collection="", trace_style_to_apply=""):
+    """
+    Iterates over all traces in the `data` list of a Plotly figure dictionary 
+    and applies styles to each one.
+
+    Args:
+        fig_dict (dict): A dictionary containing a `data` field with Plotly traces.
+        trace_style_to_apply (str): Optional style preset to apply. Default is "default".
+
+    Returns:
+        dict: Updated Plotly figure dictionary with defaults applied to each trace.
+
+    """
+    if type(trace_styles_collection) == type("string"):
+        trace_styles_collection_name = trace_styles_collection
+    else:
+        trace_styles_collection_name = trace_styles_collection["name"]
+
+    if "data" in fig_dict and isinstance(fig_dict["data"], list):
+        fig_dict["data"] = [apply_trace_style_to_single_data_series(data_series=trace,trace_styles_collection=trace_styles_collection, trace_style_to_apply=trace_style_to_apply) for trace in fig_dict["data"]]
     
+    if "plot_style" not in fig_dict:
+        fig_dict["plot_style"] = {}
+    fig_dict["plot_style"]["trace_styles_collection"] = trace_styles_collection_name
+    return fig_dict
+
 
-def apply_style_to_plotly_dict(plotly_json, style_name):
+# The logic in JSONGrapher is to apply the style information but to treat "type" differently 
+# Accordingly, we use 'trace_styles_collection' as a field in JSONGrapher for each data_series.
+# compared to how plotly treats 'type' for a data series. So later in the process, when actually plotting with plotly, the 'type' field will get overwritten.
+def apply_trace_style_to_single_data_series(data_series, trace_styles_collection="", trace_style_to_apply=""):
     """
-    Apply a predefined style to a Plotly JSON object based on a style name which may be a journal name.
+    Applies predefined styles to a single Plotly data series while preserving relevant fields.
+
+    Args:
+        data_series (dict): A dictionary representing a single Plotly data series.
+        trace_style_to_apply (str or dict): Name of the style preset or a custom style dictionary. Default is "default".
+
+    Returns:
+        dict: Updated data series with style applied.
+    """
+    if not isinstance(data_series, dict):
+        return data_series  # Return unchanged if the data series is invalid.
+    if isinstance(trace_style_to_apply, dict):#in this case, we'll set the data_series trace_style to match.
+        data_series["trace_style"] = trace_style_to_apply
+    if str(trace_style_to_apply) != str(''): #if we received a non-empty string (or dictionary), we'll put it into the data_series object.
+        data_series["trace_style"] = trace_style_to_apply
+    elif str(trace_style_to_apply) == str(''): #If we received an empty string for the trace_style_to apply (default JSONGrapher flow), we'll check in the data_series object.   
+        #first see if there is a trace_style in the data_series.
+        trace_style = data_series.get("trace_style", "")
+        #If it's "none", then we'll return the data series unchanged.
+        #We consider it that for every trace_styles_collection, that "none" means to make no change.
+        if str(trace_style).lower() == "none":
+            return data_series
+        #if we find a dictionary, we will set the trace_style_to_apply to that, to ensure we skip other string checks to use the dictionary.
+        if isinstance(trace_style,dict):
+            trace_style_to_apply = trace_style
+    #if the trace_style_to_apply is a string and we have not received a trace_styles collection, then we have nothing
+    #to use, so will return the data_series unchanged.
+    if type(trace_style_to_apply) == type("string"):
+        if (trace_styles_collection == '') or (str(trace_styles_collection).lower() == 'none'):
+            return data_series    
+    #if the trace_style_to_apply is "none", we will return the series unchanged.
+    if str(trace_style_to_apply).lower() == str("none"):
+        return data_series
+    #Add a couple of hardcoded cases.
+    if type(trace_style_to_apply) == type("string"):
+        if (trace_style_to_apply.lower() == "nature") or (trace_style_to_apply.lower() == "science"):
+            trace_style_to_apply = "default"
+
+    #at this stage, should remove any existing formatting before applying new formatting.
+    data_series = remove_trace_style_from_single_data_series(data_series)
+
+    # -------------------------------
+    # Predefined trace_styles_collection
+    # -------------------------------
+    # Each trace_styles_collection is defined as a dictionary containing multiple trace_styles.
+    # Users can select a style preset trace_styles_collection (e.g., "default", "minimalist", "bold"),
+    # and this function will apply appropriate settings for the given trace_style.
+    #
+    # Examples of Supported trace_styles:
+    # - "scatter_spline" (default when type is not specified)
+    # - "scatter"
+    # - "spline"
+    # - "bar"
+    # - "heatmap"
+    #
+    # Note: Colors are intentionally omitted to allow users to define their own.
+    # However, predefined colorscales are applied for heatmaps.
+
+
+    styles_available = JSONGrapher.styles.trace_styles_collection_library.styles_library
+
+    # Get the appropriate style dictionary
+    if isinstance(trace_styles_collection, dict):
+        styles_collection_dict = trace_styles_collection  # Use custom style directly
+    else:
+        styles_collection_dict = styles_available.get(trace_styles_collection, {})
+        if not styles_collection_dict:  # Check if it's an empty dictionary
+            print(f"Warning: trace_styles_collection named '{trace_styles_collection}' not found. Using 'default' trace_styles_collection instead.")
+            styles_collection_dict = styles_available.get("default", {})
+    # Determine the trace_style, defaulting to the first item in a given style if none is provided.
+
+    # Retrieve the specific style for the plot type
+    if trace_style_to_apply == "":# if a trace_style_to_apply has not been supplied, we will get it from the dataseries.
+        trace_style = data_series.get("trace_style", "")
+    else:
+        trace_style = trace_style_to_apply
+
+    if trace_style == "": #if the trace style is an empty string....
+        trace_style = list(styles_collection_dict.keys())[0] #take the first trace_style name in the style_dict.  In python 3.7 and later dictionary keys preserve ordering.
+
+    #If a person adds "__colorscale" to the end of a trace_style, like "scatter_spline__rainbow" we will extract the colorscale and apply it to the plot.
+    #This should be done before extracting the trace_style from the styles_available, because we need to split the string to break out the trace_style
+    colorscale = "" #initializing variable.
+    if isinstance(trace_style, str): #check if it is a string type.
+        if "__" in trace_style:
+            trace_style, colorscale = trace_style.split("__")
+
+    colorscale_structure = "" #initialize this variable for use later. It tells us which fields to put the colorscale related values in. This should be done before regular trace_style fields are applied.
+    #3D and bubble plots will have a colorscale by default.
+    if trace_style == "bubble": #for bubble trace styles, we need to move the z values into the marker size. We also need to do this before the styles_dict collection is accessed, since then the trace_style becomes a dictionary.
+        data_series = prepare_bubble_sizes(data_series)
+        colorscale_structure = "bubble"
+    elif trace_style == "mesh3d": #for bubble trace styles, we need to move the z values into the marker size. We also need to do this before the styles_dict collection is accessed, since then the trace_style becomes a dictionary.
+        colorscale_structure = "mesh3d"
+    elif trace_style == "scatter3d": #for bubble trace styles, we need to move the z values into the marker size. We also need to do this before the styles_dict collection is accessed, since then the trace_style becomes a dictionary.
+        colorscale_structure = "scatter3d"
+
+    if trace_style in styles_collection_dict:
+        trace_style = styles_collection_dict.get(trace_style)
+    elif trace_style not in styles_collection_dict:  # Check if it's an empty dictionary
+        print(f"Warning: trace_style named '{trace_style}' not found in trace_styles_collection '{trace_styles_collection}'. Using the first trace_style in in trace_styles_collection '{trace_styles_collection}'.")
+        trace_style = list(styles_collection_dict.keys())[0] #take the first trace_style name in the style_dict.  In python 3.7 and later dictionary keys preserve ordering.
+        trace_style = styles_collection_dict.get(trace_style)
+
+    # Apply type and other predefined settings
+    data_series["type"] = trace_style.get("type")  
+    # Apply other attributes while preserving existing values
+    for key, value in trace_style.items():
+        if key not in ["type"]:
+            if isinstance(value, dict):  # Ensure value is a dictionary
+                data_series.setdefault(key, {}).update(value)
+            else:
+                data_series[key] = value  # Direct assignment for non-dictionary values
+
+    #Before applying colorscales, we check if we have recieved a colorscale from the user. If so, we'll need to parse the trace_type to assign the colorscale structure.
+    if colorscale != "":
+        #If it is a scatter plot with markers, then the colorscale_structure will be marker. Need to check for this before the lines alone case.
+        if ("markers" in data_series["mode"]) or ("markers+lines" in data_series["mode"]) or ("lines+markers" in data_series["mode"]):
+            colorscale_structure = "marker"
+        elif ("lines" in data_series["mode"]):
+            colorscale_structure = "line"
+        elif ("bar" in data_series["type"]):
+            colorscale_structure = "marker"
+
+    #Block of code to clean color values for 3D plots and 2D plots. It can't be just from the style dictionary because we need to point to data.
+    def clean_color_values(list_of_values, variable_string_for_warning):
+        if None in list_of_values:
+            print("Warning: A colorscale based on" + variable_string_for_warning + "was requested. None values were found. They are being replaced with 0 values. It is recommended to provide data without None values.")
+            color_values = [0 if value is None else value for value in list_of_values]
+        else:
+            color_values = list_of_values
+        return color_values
+
+    if colorscale_structure == "bubble":
+        #data_series["marker"]["colorscale"] = "viridis_r" #https://plotly.com/python/builtin-colorscales/
+        data_series["marker"]["showscale"] = True
+        if "z" in data_series:
+            color_values = clean_color_values(list_of_values= data_series["z"], variable_string_for_warning="z")
+            data_series["marker"]["color"] = color_values
+        elif "z_points" in data_series:
+            color_values = clean_color_values(list_of_values= data_series["z_points"], variable_string_for_warning="z_points")
+            data_series["marker"]["color"] = color_values
+    elif colorscale_structure == "scatter3d":
+        #data_series["marker"]["colorscale"] = "viridis_r" #https://plotly.com/python/builtin-colorscales/
+        data_series["marker"]["showscale"] = True
+        if "z" in data_series:
+            color_values = clean_color_values(list_of_values= data_series["z"], variable_string_for_warning="z")
+            data_series["marker"]["color"] = color_values
+        elif "z_points" in data_series:
+            color_values = clean_color_values(list_of_values= data_series["z_points"], variable_string_for_warning="z_points")
+            data_series["marker"]["color"] = color_values
+    elif colorscale_structure == "mesh3d":
+        #data_series["colorscale"] = "viridis_r" #https://plotly.com/python/builtin-colorscales/
+        data_series["showscale"] = True
+        if "z" in data_series:
+            color_values = clean_color_values(list_of_values= data_series["z"], variable_string_for_warning="z")
+            data_series["intensity"] = color_values
+        elif "z_points" in data_series:
+            color_values = clean_color_values(list_of_values= data_series["z_points"], variable_string_for_warning="z_points")
+            data_series["intensity"] = color_values
+    elif colorscale_structure == "marker":
+        data_series["marker"]["colorscale"] = colorscale
+        data_series["marker"]["showscale"] = True
+        color_values = clean_color_values(list_of_values=data_series["y"], variable_string_for_warning="y")
+        data_series["marker"]["color"] = color_values
+    elif colorscale_structure == "line":
+        data_series["line"]["colorscale"] = colorscale
+        data_series["line"]["showscale"] = True
+        color_values = clean_color_values(list_of_values=data_series["y"], variable_string_for_warning="y")
+        data_series["line"]["color"] = color_values
+        
+            
+    return data_series
+
+def prepare_bubble_sizes(data_series):
+    #To make a bubble plot with plotly, we are actually using a 2D plot
+    #and are using the z values in a data_series to create the sizes of each point.
+    #We also will scale them to some maximum bubble size that is specifed.
+    if "marker" not in data_series:
+        data_series["marker"] = {}   
+    if "z_points" in data_series:
+        data_series["marker"]["size"] = data_series["z_points"]
+    elif "z" in data_series:
+        data_series["marker"]["size"] = data_series["z"]
+
+    #now need to normalize to the max value in the list.
+    def normalize_to_max(starting_list):
+        import numpy as np
+        arr = np.array(starting_list)  # Convert list to NumPy array for efficient operations
+        max_value = np.max(arr)  # Find the maximum value in the list
+        if max_value == 0:
+            normalized_values = np.zeros_like(arr)  # If max_value is zero, return zeros
+        else:
+            normalized_values = arr / max_value  # Otherwise, divide each element by max_value           
+        return normalized_values  # Return the normalized values
+    try:
+        normalized_sizes = normalize_to_max(data_series["marker"]["size"])
+    except KeyError as exc:
+        raise KeyError("Error: During bubble plot bubble size normalization, there was an error. This usually means the z variable has not been populated. For example, by equation evaluation set to false or simulation evaluation set to false.")
+
+        
+    #Now biggest bubble is 1 (or 0) so multiply to enlarge to scale.
+    if "max_bubble_size" in data_series:
+        max_bubble_size = data_series["max_bubble_size"]
+    else:
+        max_bubble_size = 10       
+    scaled_sizes = normalized_sizes*max_bubble_size
+    data_series["marker"]["size"] = scaled_sizes.tolist() #from numpy array back to list.
     
-    :param plotly_json: dict, Plotly JSON object.
-    :param style_name: str, Name of the style or journal.
-    :return: dict, Updated Plotly JSON object.
+    #Now let's also set the text that appears during hovering to include the original data.
+    if "z_points" in data_series:
+        data_series["text"] = data_series["z_points"]
+    elif "z" in data_series:
+        data_series["text"] = data_series["z"]
+
+    return data_series
+
+
+#TODO: This logic should be changed in the future. There should be a separated function to remove formatting
+# versus just removing the current setting of "trace_styles_collection"
+# So the main class function will also be broken into two and/or need to take an optional argument in
+def remove_trace_styles_collection_from_plotly_dict(fig_dict):
     """
-    styles_available = {
-        "Nature": {
-            "layout": {
-                "title": {"font": {"size": 24, "family": "Times New Roman", "color": "black"}},
-                "font": {"size": 18, "family": "Times New Roman"},
-                "paper_bgcolor": "white",
-                "plot_bgcolor": "white",
-            }
-        },
-        "Science": {
-            "layout": {
-                "title": {"font": {"size": 22, "family": "Arial", "color": "black"}},
-                "font": {"size": 16, "family": "Arial"},
-                "paper_bgcolor": "white",
-                "plot_bgcolor": "white",
+    Remove applied data series styles from a Plotly figure dictionary.
+    
+    :param fig_dict: dict, Plotly style fig_dict
+    :return: dict, Updated Plotly style fig_dict with default formatting.
+    """
+    #will remove formatting from the individual data_series, but will not remove formatting from any that have trace_style of "none".
+    if isinstance(fig_dict, dict) and "data" in fig_dict and isinstance(fig_dict["data"], list):
+        updated_data = []  # Initialize an empty list to store processed traces
+        for trace in fig_dict["data"]:
+            # Check if the trace has a "trace_style" field and if its value is "none" (case-insensitive)
+            if trace.get("trace_style", "").lower() == "none":
+                updated_data.append(trace)  # Skip modification and keep the trace unchanged
+            else:
+                # Apply the function to modify the trace before adding it to the list
+                updated_data.append(remove_trace_style_from_single_data_series(trace))
+        # Update the "data" field with the processed traces
+        fig_dict["data"] = updated_data
+
+
+    #If being told to remove the style, should also pop it from fig_dict.
+    if "plot_style" in fig_dict:
+        if "trace_styles_collection" in fig_dict["plot_style"]:
+            fig_dict["plot_style"].pop("trace_styles_collection")
+    return fig_dict
+
+def remove_trace_style_from_single_data_series(data_series):
+    """
+    Remove only formatting fields from a single Plotly data series while preserving all other fields.
+
+    Note: Since fig_dict data objects may contain custom fields (e.g., "equation", "metadata"),
+    this function explicitly removes predefined **formatting** attributes while leaving all other data intact.
+
+    :param data_series: dict, A dictionary representing a single Plotly data series.
+    :return: dict, Updated data series with formatting fields removed but key data retained.
+    """
+
+    if not isinstance(data_series, dict):
+        return data_series  # Return unchanged if input is invalid.
+
+    # **Define formatting fields to remove**
+    formatting_fields = {
+        "mode", "line", "marker", "colorscale", "opacity", "fill", "fillcolor", "color", "intensity", "showscale",
+        "legendgroup", "showlegend", "textposition", "textfont", "visible", "connectgaps", "cliponaxis", "showgrid"
+    }
+
+    # **Create a new data series excluding only formatting fields**
+    cleaned_data_series = {key: value for key, value in data_series.items() if key not in formatting_fields}
+    #make the new data series into a JSONGrapherDataSeries object.
+    new_data_series_object = JSONGrapherDataSeries()
+    new_data_series_object.update_while_preserving_old_terms(cleaned_data_series)
+    return new_data_series_object
+
+def extract_trace_style_by_index(fig_dict, data_series_index, new_trace_style_name='', extract_colors=False):
+    data_series_dict = fig_dict["data"][data_series_index]
+    extracted_trace_style = extract_trace_style_from_data_series_dict(data_series_dict=data_series_dict, new_trace_style_name=new_trace_style_name, extract_colors=extract_colors)
+    return extracted_trace_style
+
+def extract_trace_style_from_data_series_dict(data_series_dict, new_trace_style_name='', additional_attributes_to_extract=None, extract_colors=False):
+    """
+    Extract formatting attributes from a given Plotly data series.
+
+    The function scans the provided `data_series` dictionary and returns a new dictionary
+    containing only the predefined formatting fields.
+
+    Examples of formatting attributes extracted:
+    - "type"
+    - "mode"
+    - "line"
+    - "marker"
+    - "colorscale"
+    - "opacity"
+    - "fill"
+    - "legendgroup"
+    - "showlegend"
+    - "textposition"
+    - "textfont"
+
+    :param data_series_dict: dict, A dictionary representing a single Plotly data series.
+    :param trace_style: string, the key name for what user wants to call the trace_style in the style, after extraction.
+    :return: dict, A dictionary containing only the formatting attributes.
+    """  
+    if additional_attributes_to_extract is None: #in python, it's not good to make an empty list a default argument.
+        additional_attributes_to_extract = []
+
+    if new_trace_style_name=='':
+        new_trace_style_name = data_series_dict.get("trace_style", "") #keep blank if not present.
+    if new_trace_style_name=='':
+        new_trace_style_name = "custom"
+
+    if not isinstance(data_series_dict, dict):
+        return {}  # Return an empty dictionary if input is invalid.
+
+    # Define known formatting attributes. This is a set (not a dictionary, not a list)
+    formatting_fields = {
+        "type", "mode", "line", "marker", "colorscale", "opacity", "fill", "fillcolor", "color", "intensity", "showscale",
+        "legendgroup", "showlegend", "textposition", "textfont", "visible", "connectgaps", "cliponaxis", "showgrid"
+    }
+
+    formatting_fields.update(additional_attributes_to_extract)
+    # Extract only formatting-related attributes
+    trace_style_dict = {key: value for key, value in data_series_dict.items() if key in formatting_fields}
+
+    #Pop out colors if we are not extracting them.
+    if extract_colors == False:
+        if "marker" in trace_style_dict:
+            if "color" in trace_style_dict["marker"]:
+                trace_style_dict["marker"].pop("color")
+        if "line" in trace_style_dict:
+            if "color" in trace_style_dict["line"]:
+                trace_style_dict["line"].pop("color")
+        if "colorscale" in trace_style_dict:  # Handles top-level colorscale for heatmaps, choropleths
+            trace_style_dict.pop("colorscale")
+        if "fillcolor" in trace_style_dict:  # Handles fill colors
+            trace_style_dict.pop("fillcolor")
+        if "textfont" in trace_style_dict:
+            if "color" in trace_style_dict["textfont"]:  # Handles text color
+                trace_style_dict["textfont"].pop("color")
+        if "legendgrouptitle" in trace_style_dict and isinstance(trace_style_dict["legendgrouptitle"], dict):
+            if "font" in trace_style_dict["legendgrouptitle"] and isinstance(trace_style_dict["legendgrouptitle"]["font"], dict):
+                if "color" in trace_style_dict["legendgrouptitle"]["font"]:
+                    trace_style_dict["legendgrouptitle"]["font"].pop("color")
+    extracted_trace_style = {new_trace_style_name : trace_style_dict} #this is a trace_style dict.
+    return extracted_trace_style #this is a trace_style dict.
+
+#export a single trace_style dictionary to .json.
+def write_trace_style_to_file(trace_style_dict, trace_style_name, filename):
+    # Ensure the filename ends with .json
+    if not filename.lower().endswith(".json"):
+        filename += ".json"
+
+    json_structure = {
+        "trace_style": {
+            "name": trace_style_name,
+            trace_style_name: {
+                trace_style_dict
             }
         }
     }
 
-    # Get the style for the specified journal, default to no change if not found
-    style_dict = styles_available.get(style_name, {})
-    
-    # Ensure title field is merged properly to avoid overwriting
-    plotly_json.setdefault("layout", {})
-    plotly_json["layout"].setdefault("title", {})
-    
-    # Merge title settings separately to preserve existing text
-    plotly_json["layout"]["title"] = {**plotly_json["layout"]["title"], **style_dict.get("layout", {}).get("title", {})}
+    with open(filename, "w", encoding="utf-8") as file:  # Specify UTF-8 encoding for compatibility
+        json.dump(json_structure, file, indent=4)
+
+
+#export an entire trace_styles_collection to .json. The trace_styles_collection is dict.
+def write_trace_styles_collection_to_file(trace_styles_collection, trace_styles_collection_name, filename):   
+    if "trace_styles_collection" in trace_styles_collection: #We may receive a traces_style collection in a container. If so, we pull the traces_style_collection out.
+        trace_styles_collection = trace_styles_collection[trace_styles_collection["name"]] 
+    # Ensure the filename ends with .json
+    if not filename.lower().endswith(".json"):
+        filename += ".json"
+
+    json_structure = {
+        "trace_styles_collection": {
+            "name": trace_styles_collection_name,
+            trace_styles_collection_name: trace_styles_collection
+        }
+    }
+
+    with open(filename, "w", encoding="utf-8") as file:  # Specify UTF-8 encoding for compatibility
+        json.dump(json_structure, file, indent=4)
+
+
+
+#export an entire trace_styles_collection from .json. THe trace_styles_collection is dict.
+def import_trace_styles_collection(filename):
+    # Ensure the filename ends with .json
+    if not filename.lower().endswith(".json"):
+        filename += ".json"
+
+    with open(filename, "r", encoding="utf-8") as file:  # Specify UTF-8 encoding for compatibility
+        data = json.load(file)
+
+    # Validate JSON structure
+    containing_dict = data.get("trace_styles_collection")
+    if not isinstance(containing_dict, dict):
+        raise ValueError("Error: Missing or malformed 'trace_styles_collection'.")
+
+    collection_name = containing_dict.get("name")
+    if not isinstance(collection_name, str) or collection_name not in containing_dict:
+        raise ValueError(f"Error: Expected dictionary '{collection_name}' is missing or malformed.")
+    trace_styles_collection  = containing_dict[collection_name]
+    # Return only the dictionary corresponding to the collection name
+    return trace_styles_collection
+
+
+#export an entire trace_styles_collection from .json. THe trace_styles_collection is dict.
+def import_trace_style(filename):
+    # Ensure the filename ends with .json
+    if not filename.lower().endswith(".json"):
+        filename += ".json"
+
+    with open(filename, "r", encoding="utf-8") as file:  # Specify UTF-8 encoding for compatibility
+        data = json.load(file)
+
+    # Validate JSON structure
+    containing_dict = data.get("trace_style")
+    if not isinstance(containing_dict, dict):
+        raise ValueError("Error: Missing or malformed 'trace_style'.")
+
+    style_name = containing_dict.get("name")
+    if not isinstance(style_name, str) or style_name not in containing_dict:
+        raise ValueError(f"Error: Expected dictionary '{style_name}' is missing or malformed.")
+    trace_style_dict = containing_dict[style_name]
+
+    # Return only the dictionary corresponding to the trace style name
+    return trace_style_dict
+
+
+def apply_layout_style_to_plotly_dict(fig_dict, layout_style_to_apply="default"):
+    """
+    Apply a predefined style to a Plotly fig_dict while preserving non-cosmetic fields.
     
-    # Merge other layout settings
-    for key, value in style_dict.get("layout", {}).items():
-        if key != "title":  # Skip title since it was handled separately
-            plotly_json["layout"][key] = value
+    :param fig_dict: dict, Plotly style fig_dict
+    :param layout_style_to_apply: str, Name of the style or journal, or a style dictionary to apply.
+    :return: dict, Updated Plotly style fig_dict.
+    """
+    if type(layout_style_to_apply) == type("string"):
+        layout_style_to_apply_name = layout_style_to_apply
+    else:
+        layout_style_to_apply_name = list(layout_style_to_apply.keys())[0]#if it is a dictionary, it will have one key which is its name.
+    if (layout_style_to_apply == '') or (str(layout_style_to_apply).lower() == 'none'):
+        return fig_dict
+
+    #Hardcoding some cases as ones that will call the default layout, for convenience.
+    if (layout_style_to_apply.lower() == "minimalist") or (layout_style_to_apply.lower() == "bold"):
+        layout_style_to_apply = "default"
+
+
+    styles_available = JSONGrapher.styles.layout_styles_library.styles_library
+
+
+    # Use or get the style specified, or use default if not found
+    if isinstance(layout_style_to_apply, dict):
+        style_dict = layout_style_to_apply
+    else:
+        style_dict = styles_available.get(layout_style_to_apply, {})
+        if not style_dict:  # Check if it's an empty dictionary
+            print(f"Style named '{layout_style_to_apply}' not found with explicit layout dictionary. Using 'default' layout style.")
+            style_dict = styles_available.get("default", {})
+
+    # Ensure layout exists in the figure
+    fig_dict.setdefault("layout", {})
+
+    # **Extract non-cosmetic fields**
+    non_cosmetic_fields = {
+        "title.text": fig_dict.get("layout", {}).get("title", {}).get("text", None),
+        "xaxis.title.text": fig_dict.get("layout", {}).get("xaxis", {}).get("title", {}).get("text", None),
+        "yaxis.title.text": fig_dict.get("layout", {}).get("yaxis", {}).get("title", {}).get("text", None),
+        "zaxis.title.text": fig_dict.get("layout", {}).get("zaxis", {}).get("title", {}).get("text", None),
+        "legend.title.text": fig_dict.get("layout", {}).get("legend", {}).get("title", {}).get("text", None),
+        "annotations.text": [
+            annotation.get("text", None) for annotation in fig_dict.get("layout", {}).get("annotations", [])
+        ],
+        "updatemenus.buttons.label": [
+            button.get("label", None) for menu in fig_dict.get("layout", {}).get("updatemenus", [])
+            for button in menu.get("buttons", [])
+        ],
+        "coloraxis.colorbar.title.text": fig_dict.get("layout", {}).get("coloraxis", {}).get("colorbar", {}).get("title", {}).get("text", None),
+    }
+
+    # **Apply style dictionary to create a fresh layout object**
+    new_layout = style_dict.get("layout", {}).copy()
+
+    # **Restore non-cosmetic fields**
+    if non_cosmetic_fields["title.text"]:
+        new_layout.setdefault("title", {})["text"] = non_cosmetic_fields["title.text"]
+
+    if non_cosmetic_fields["xaxis.title.text"]:
+        new_layout.setdefault("xaxis", {}).setdefault("title", {})["text"] = non_cosmetic_fields["xaxis.title.text"]
+
+    if non_cosmetic_fields["yaxis.title.text"]:
+        new_layout.setdefault("yaxis", {}).setdefault("title", {})["text"] = non_cosmetic_fields["yaxis.title.text"]
+
+    if non_cosmetic_fields["zaxis.title.text"]:
+        new_layout.setdefault("zaxis", {}).setdefault("title", {})["text"] = non_cosmetic_fields["zaxis.title.text"]
+
+    if non_cosmetic_fields["legend.title.text"]:
+        new_layout.setdefault("legend", {}).setdefault("title", {})["text"] = non_cosmetic_fields["legend.title.text"]
+
+    if non_cosmetic_fields["annotations.text"]:
+        new_layout["annotations"] = [{"text": text} for text in non_cosmetic_fields["annotations.text"]]
+
+    if non_cosmetic_fields["updatemenus.buttons.label"]:
+        new_layout["updatemenus"] = [{"buttons": [{"label": label} for label in non_cosmetic_fields["updatemenus.buttons.label"]]}]
+
+    if non_cosmetic_fields["coloraxis.colorbar.title.text"]:
+        new_layout.setdefault("coloraxis", {}).setdefault("colorbar", {})["title"] = {"text": non_cosmetic_fields["coloraxis.colorbar.title.text"]}
+
+    # **Assign the new layout back into the figure dictionary**
+    fig_dict["layout"] = new_layout
+    #Now update the fig_dict to signify the new layout_style used.
+    if "plot_style" not in fig_dict:
+        fig_dict["plot_style"] = {}
+    fig_dict["plot_style"]["layout_style"] = layout_style_to_apply_name
+    return fig_dict
+
+#TODO: This logic should be changed in the future. There should be a separated function to remove formatting
+# versus just removing the current setting of "layout_style"
+# So the main class function will also be broken into two and/or need to take an optional argument in
+def remove_layout_style_from_plotly_dict(fig_dict):
+    """
+    Remove applied layout styles from a Plotly figure dictionary while preserving essential content.
+
+    :param fig_dict: dict, Plotly style fig_dict
+    :return: dict, Updated Plotly style fig_dict with styles removed but key data intact.
+    """
+    if "layout" in fig_dict:
+        style_keys = ["font", "paper_bgcolor", "plot_bgcolor", "gridcolor", "gridwidth", "tickfont", "linewidth"]
+
+        # **Store non-cosmetic fields if present, otherwise assign None**
+        non_cosmetic_fields = {
+            "title.text": fig_dict.get("layout", {}).get("title", {}).get("text", None),
+            "xaxis.title.text": fig_dict.get("layout", {}).get("xaxis", {}).get("title", {}).get("text", None),
+            "yaxis.title.text": fig_dict.get("layout", {}).get("yaxis", {}).get("title", {}).get("text", None),
+            "zaxis.title.text": fig_dict.get("layout", {}).get("zaxis", {}).get("title", {}).get("text", None),
+            "legend.title.text": fig_dict.get("layout", {}).get("legend", {}).get("title", {}).get("text", None),
+            "annotations.text": [annotation.get("text", None) for annotation in fig_dict.get("layout", {}).get("annotations", [])],
+            "updatemenus.buttons.label": [
+                button.get("label", None) for menu in fig_dict.get("layout", {}).get("updatemenus", [])
+                for button in menu.get("buttons", [])
+            ],
+            "coloraxis.colorbar.title.text": fig_dict.get("layout", {}).get("coloraxis", {}).get("colorbar", {}).get("title", {}).get("text", None),
+        }
+
+        # Preserve title text while removing font styling
+        if "title" in fig_dict["layout"] and isinstance(fig_dict["layout"]["title"], dict):
+            fig_dict["layout"]["title"] = {"text": non_cosmetic_fields["title.text"]} if non_cosmetic_fields["title.text"] is not None else {}
+
+        # Preserve axis titles while stripping font styles
+        for axis in ["xaxis", "yaxis", "zaxis"]:
+            if axis in fig_dict["layout"] and isinstance(fig_dict["layout"][axis], dict):
+                if "title" in fig_dict["layout"][axis] and isinstance(fig_dict["layout"][axis]["title"], dict):
+                    fig_dict["layout"][axis]["title"] = {"text": non_cosmetic_fields[f"{axis}.title.text"]} if non_cosmetic_fields[f"{axis}.title.text"] is not None else {}
+
+                # Remove style-related attributes but keep axis configurations
+                for key in style_keys:
+                    fig_dict["layout"][axis].pop(key, None)
+
+        # Preserve legend title text while stripping font styling
+        if "legend" in fig_dict["layout"] and isinstance(fig_dict["layout"]["legend"], dict):
+            if "title" in fig_dict["layout"]["legend"] and isinstance(fig_dict["layout"]["legend"]["title"], dict):
+                fig_dict["layout"]["legend"]["title"] = {"text": non_cosmetic_fields["legend.title.text"]} if non_cosmetic_fields["legend.title.text"] is not None else {}
+            fig_dict["layout"]["legend"].pop("font", None)
+
+        # Preserve annotations text while stripping style attributes
+        if "annotations" in fig_dict["layout"]:
+            fig_dict["layout"]["annotations"] = [
+                {"text": text} if text is not None else {} for text in non_cosmetic_fields["annotations.text"]
+            ]
+
+        # Preserve update menu labels while stripping styles
+        if "updatemenus" in fig_dict["layout"]:
+            for menu in fig_dict["layout"]["updatemenus"]:
+                for i, button in enumerate(menu.get("buttons", [])):
+                    button.clear()
+                    if non_cosmetic_fields["updatemenus.buttons.label"][i] is not None:
+                        button["label"] = non_cosmetic_fields["updatemenus.buttons.label"][i]
+
+        # Preserve color bar title while stripping styles
+        if "coloraxis" in fig_dict["layout"] and "colorbar" in fig_dict["layout"]["coloraxis"]:
+            fig_dict["layout"]["coloraxis"]["colorbar"]["title"] = {"text": non_cosmetic_fields["coloraxis.colorbar.title.text"]} if non_cosmetic_fields["coloraxis.colorbar.title.text"] is not None else {}
+
+        # Remove general style settings without clearing layout structure
+        for key in style_keys:
+            fig_dict["layout"].pop(key, None)
+
+    #If being told to remove the style, should also pop it from fig_dict.
+    if "plot_style" in fig_dict:
+        if "layout_style" in fig_dict["plot_style"]:
+            fig_dict["plot_style"].pop("layout_style")
+    return fig_dict
+
+def extract_layout_style_from_plotly_dict(fig_dict):
+    """
+    Extract a layout style dictionary from a given Plotly JSON object, including background color, grids, and other appearance attributes.
+
+    :param fig_dict: dict, Plotly JSON object.
+    :return: dict, Extracted style settings.
+    """
+
+
+    # **Extraction Phase** - Collect cosmetic fields if they exist
+    layout = fig_dict.get("layout", {})
+
+    # Note: Each assignment below will return None if the corresponding field is missing
+    title_font = layout.get("title", {}).get("font")
+    title_x = layout.get("title", {}).get("x")
+    title_y = layout.get("title", {}).get("y")
+
+    global_font = layout.get("font")
+    paper_bgcolor = layout.get("paper_bgcolor")
+    plot_bgcolor = layout.get("plot_bgcolor")
+    margin = layout.get("margin")
+
+    # Extract x-axis cosmetic fields
+    xaxis_title_font = layout.get("xaxis", {}).get("title", {}).get("font")
+    xaxis_tickfont = layout.get("xaxis", {}).get("tickfont")
+    xaxis_gridcolor = layout.get("xaxis", {}).get("gridcolor")
+    xaxis_gridwidth = layout.get("xaxis", {}).get("gridwidth")
+    xaxis_zerolinecolor = layout.get("xaxis", {}).get("zerolinecolor")
+    xaxis_zerolinewidth = layout.get("xaxis", {}).get("zerolinewidth")
+    xaxis_tickangle = layout.get("xaxis", {}).get("tickangle")
+
+    # **Set flag for x-axis extraction**
+    xaxis = any([
+        xaxis_title_font, xaxis_tickfont, xaxis_gridcolor, xaxis_gridwidth,
+        xaxis_zerolinecolor, xaxis_zerolinewidth, xaxis_tickangle
+    ])
+
+    # Extract y-axis cosmetic fields
+    yaxis_title_font = layout.get("yaxis", {}).get("title", {}).get("font")
+    yaxis_tickfont = layout.get("yaxis", {}).get("tickfont")
+    yaxis_gridcolor = layout.get("yaxis", {}).get("gridcolor")
+    yaxis_gridwidth = layout.get("yaxis", {}).get("gridwidth")
+    yaxis_zerolinecolor = layout.get("yaxis", {}).get("zerolinecolor")
+    yaxis_zerolinewidth = layout.get("yaxis", {}).get("zerolinewidth")
+    yaxis_tickangle = layout.get("yaxis", {}).get("tickangle")
+
+    # **Set flag for y-axis extraction**
+    yaxis = any([
+        yaxis_title_font, yaxis_tickfont, yaxis_gridcolor, yaxis_gridwidth,
+        yaxis_zerolinecolor, yaxis_zerolinewidth, yaxis_tickangle
+    ])
+
+    # Extract legend styling
+    legend_font = layout.get("legend", {}).get("font")
+    legend_x = layout.get("legend", {}).get("x")
+    legend_y = layout.get("legend", {}).get("y")
+
+    # **Assignment Phase** - Reconstruct dictionary in a structured manner
+    extracted_layout_style = {"layout": {}}
+
+    if title_font or title_x:
+        extracted_layout_style["layout"]["title"] = {}
+        if title_font:
+            extracted_layout_style["layout"]["title"]["font"] = title_font
+        if title_x:
+            extracted_layout_style["layout"]["title"]["x"] = title_x
+        if title_y:
+            extracted_layout_style["layout"]["title"]["y"] = title_y
+
+    if global_font:
+        extracted_layout_style["layout"]["font"] = global_font
+
+    if paper_bgcolor:
+        extracted_layout_style["layout"]["paper_bgcolor"] = paper_bgcolor
+    if plot_bgcolor:
+        extracted_layout_style["layout"]["plot_bgcolor"] = plot_bgcolor
+    if margin:
+        extracted_layout_style["layout"]["margin"] = margin
+
+    if xaxis:
+        extracted_layout_style["layout"]["xaxis"] = {}
+        if xaxis_title_font:
+            extracted_layout_style["layout"]["xaxis"]["title"] = {"font": xaxis_title_font}
+        if xaxis_tickfont:
+            extracted_layout_style["layout"]["xaxis"]["tickfont"] = xaxis_tickfont
+        if xaxis_gridcolor:
+            extracted_layout_style["layout"]["xaxis"]["gridcolor"] = xaxis_gridcolor
+        if xaxis_gridwidth:
+            extracted_layout_style["layout"]["xaxis"]["gridwidth"] = xaxis_gridwidth
+        if xaxis_zerolinecolor:
+            extracted_layout_style["layout"]["xaxis"]["zerolinecolor"] = xaxis_zerolinecolor
+        if xaxis_zerolinewidth:
+            extracted_layout_style["layout"]["xaxis"]["zerolinewidth"] = xaxis_zerolinewidth
+        if xaxis_tickangle:
+            extracted_layout_style["layout"]["xaxis"]["tickangle"] = xaxis_tickangle
+
+    if yaxis:
+        extracted_layout_style["layout"]["yaxis"] = {}
+        if yaxis_title_font:
+            extracted_layout_style["layout"]["yaxis"]["title"] = {"font": yaxis_title_font}
+        if yaxis_tickfont:
+            extracted_layout_style["layout"]["yaxis"]["tickfont"] = yaxis_tickfont
+        if yaxis_gridcolor:
+            extracted_layout_style["layout"]["yaxis"]["gridcolor"] = yaxis_gridcolor
+        if yaxis_gridwidth:
+            extracted_layout_style["layout"]["yaxis"]["gridwidth"] = yaxis_gridwidth
+        if yaxis_zerolinecolor:
+            extracted_layout_style["layout"]["yaxis"]["zerolinecolor"] = yaxis_zerolinecolor
+        if yaxis_zerolinewidth:
+            extracted_layout_style["layout"]["yaxis"]["zerolinewidth"] = yaxis_zerolinewidth
+        if yaxis_tickangle:
+            extracted_layout_style["layout"]["yaxis"]["tickangle"] = yaxis_tickangle
+
+    if legend_font or legend_x or legend_y:
+        extracted_layout_style["layout"]["legend"] = {}
+        if legend_font:
+            extracted_layout_style["layout"]["legend"]["font"] = legend_font
+        if legend_x:
+            extracted_layout_style["layout"]["legend"]["x"] = legend_x
+        if legend_y:
+            extracted_layout_style["layout"]["legend"]["y"] = legend_y
+
+    return extracted_layout_style
+
+## Start of Section of Code for Styles and Converting between plotly and matplotlib Fig objectss ##
+
+### Start of section of code with functions for extracting and updating x and y ranges of data series ###
+
+def update_implicit_data_series_x_ranges(fig_dict, range_dict):
+    """
+    Updates the x_range_default values for all simulate and equation data series 
+    in a given figure dictionary using the provided range dictionary.
+
+    Args:
+        fig_dict (dict): The original figure dictionary containing various data series.
+        range_dict (dict): A dictionary with keys "min_x" and "max_x" providing the 
+                           global minimum and maximum x values for updates.
+
+    Returns:
+        dict: A new figure dictionary with updated x_range_default values for 
+              equation and simulate series, while keeping other data unchanged.
     
-    return plotly_json
+    Notes:
+        - If min_x or max_x in range_dict is None, the function preserves the 
+          existing x_range_default values instead of overwriting them.
+        - Uses deepcopy to ensure modifications do not affect the original fig_dict.
+    """
+    import copy  # Import inside function to limit scope
+
+    updated_fig_dict = copy.deepcopy(fig_dict)  # Deep copy avoids modifying original data
+
+    min_x = range_dict["min_x"]
+    max_x = range_dict["max_x"]
+
+    for data_series in updated_fig_dict.get("data", []):
+        if "equation" in data_series:
+            equation_info = data_series["equation"]
+
+            # Determine valid values before assignment
+            min_x_value = min_x if (min_x is not None) else equation_info.get("x_range_default", [None, None])[0]
+            max_x_value = max_x if (max_x is not None) else equation_info.get("x_range_default", [None, None])[1]
+
+            # Assign updated values
+            equation_info["x_range_default"] = [min_x_value, max_x_value]
+        
+        elif "simulate" in data_series:
+            simulate_info = data_series["simulate"]
+
+            # Determine valid values before assignment
+            min_x_value = min_x if (min_x is not None) else simulate_info.get("x_range_default", [None, None])[0]
+            max_x_value = max_x if (max_x is not None) else simulate_info.get("x_range_default", [None, None])[1]
+
+            # Assign updated values
+            simulate_info["x_range_default"] = [min_x_value, max_x_value]
+
+    return updated_fig_dict
+
+
+
+
+def get_fig_dict_ranges(fig_dict, skip_equations=False, skip_simulations=False):
+    """
+    Extracts minimum and maximum x/y values from each data_series in a fig_dict, as well as overall min and max for x and y.
+
+    Args:
+        fig_dict (dict): The figure dictionary containing multiple data series.
+        skip_equations (bool): If True, equation-based data series are ignored.
+        skip_simulations (bool): If True, simulation-based data series are ignored.
+
+    Returns:
+        tuple: 
+            - fig_dict_ranges (dict): A dictionary containing overall min/max x/y values across all valid series.
+            - data_series_ranges (dict): A dictionary with individual min/max values for each data series.
+
+    Notes:
+        - Equations and simulations have predefined x-range defaults and limits.
+        - If their x-range is absent, individual data series values are used.
+        - Ensures empty lists don't trigger errors when computing min/max values.
+    """
+    # Initialize final range values to None to ensure assignment
+    fig_dict_ranges = {
+        "min_x": None,
+        "max_x": None,
+        "min_y": None,
+        "max_y": None
+    }
+
+    data_series_ranges = {
+        "min_x": [],
+        "max_x": [],
+        "min_y": [],
+        "max_y": []
+    }
+
+    for data_series in fig_dict.get("data", []):
+        min_x, max_x, min_y, max_y = None, None, None, None  # Initialize extrema as None
+
+        # Determine if the data series contains either "equation" or "simulate"
+        if "equation" in data_series:
+            if skip_equations:
+                implicit_data_series_to_extract_from = None
+                # Will Skip processing, but still append None values
+            else:
+                implicit_data_series_to_extract_from = data_series["equation"]
+        
+        elif "simulate" in data_series:
+            if skip_simulations:
+                implicit_data_series_to_extract_from = None
+                # Will Skip processing, but still append None values
+            else:
+                implicit_data_series_to_extract_from = data_series["simulate"]
+        
+        else:
+            implicit_data_series_to_extract_from = None  # No equation or simulation, process x and y normally
+
+        if implicit_data_series_to_extract_from:
+            x_range_default = implicit_data_series_to_extract_from.get("x_range_default", [None, None]) 
+            x_range_limits = implicit_data_series_to_extract_from.get("x_range_limits", [None, None]) 
+
+            # Assign values, but keep None if missing
+            min_x = (x_range_default[0] if (x_range_default[0] is not None) else x_range_limits[0])
+            max_x = (x_range_default[1] if (x_range_default[1] is not None) else x_range_limits[1])
+
+        # Ensure "x" key exists AND list is not empty before calling min() or max()
+        if (min_x is None) and ("x" in data_series) and (len(data_series["x"]) > 0):  
+            valid_x_values = [x for x in data_series["x"] if x is not None]  # Filter out None values
+            if valid_x_values:  # Ensure list isn't empty after filtering
+                min_x = min(valid_x_values)  
+
+        if (max_x is None) and ("x" in data_series) and (len(data_series["x"]) > 0):  
+            valid_x_values = [x for x in data_series["x"] if x is not None]  # Filter out None values
+            if valid_x_values:  # Ensure list isn't empty after filtering
+                max_x = max(valid_x_values)  
+
+        # Ensure "y" key exists AND list is not empty before calling min() or max()
+        if (min_y is None) and ("y" in data_series) and (len(data_series["y"]) > 0):  
+            valid_y_values = [y for y in data_series["y"] if y is not None]  # Filter out None values
+            if valid_y_values:  # Ensure list isn't empty after filtering
+                min_y = min(valid_y_values)  
+
+        if (max_y is None) and ("y" in data_series) and (len(data_series["y"]) > 0):  
+            valid_y_values = [y for y in data_series["y"] if y is not None]  # Filter out None values
+            if valid_y_values:  # Ensure list isn't empty after filtering
+                max_y = max(valid_y_values)  
+
+        # Always add values to the lists, including None if applicable
+        data_series_ranges["min_x"].append(min_x)
+        data_series_ranges["max_x"].append(max_x)
+        data_series_ranges["min_y"].append(min_y)
+        data_series_ranges["max_y"].append(max_y)
+
+    # Filter out None values for overall min/max calculations
+    valid_min_x_values = [x for x in data_series_ranges["min_x"] if x is not None]
+    valid_max_x_values = [x for x in data_series_ranges["max_x"] if x is not None]
+    valid_min_y_values = [y for y in data_series_ranges["min_y"] if y is not None]
+    valid_max_y_values = [y for y in data_series_ranges["max_y"] if y is not None]
+
+    fig_dict_ranges["min_x"] = min(valid_min_x_values) if valid_min_x_values else None
+    fig_dict_ranges["max_x"] = max(valid_max_x_values) if valid_max_x_values else None
+    fig_dict_ranges["min_y"] = min(valid_min_y_values) if valid_min_y_values else None
+    fig_dict_ranges["max_y"] = max(valid_max_y_values) if valid_max_y_values else None
+
+    return fig_dict_ranges, data_series_ranges
+
+
+# # Example usage
+# fig_dict = {
+#     "data": [
+#         {"x": [1, 2, 3, 4], "y": [10, 20, 30, 40]},
+#         {"x": [5, 6, 7, 8], "y": [50, 60, 70, 80]},
+#         {"equation": {
+#             "x_range_default": [None, 500],
+#             "x_range_limits": [100, 600]
+#         }},
+#         {"simulate": {
+#             "x_range_default": [None, 700],
+#             "x_range_limits": [300, 900]
+#         }}
+#     ]
+# }
+
+# fig_dict_ranges, data_series_ranges = get_fig_dict_ranges(fig_dict, skip_equations=True, skip_simulations=True)  # Skips both
+# print("Data Series Values:", data_series_ranges)
+# print("Extreme Values:", fig_dict_ranges)
+
+### Start of section of code with functions for extracting and updating x and y ranges of data series ###
 
 
 ### Start section of code with functions for cleaning fig_dicts for plotly compatibility ###
 
-def update_title_field(data, depth=1, max_depth=10):
+def update_title_field(fig_dict, depth=1, max_depth=10):
     """ This function is intended to make JSONGrapher .json files compatible with the newer plotly recommended title field formatting
-    which is necessary to do things like change the font, and also necessary for being able to convert a JSONGrapher json_dict to python plotly figure objects. """
-    """ Recursively checks for 'title' fields and converts them to dictionary format. """
-    if depth > max_depth or not isinstance(data, dict):
-        return data
+    which is necessary to do things like change the font, and also necessary for being able to convert a JSONGrapher json_dict to python plotly figure objects.
+    Recursively checks for 'title' fields and converts them to dictionary format. """
+    if depth > max_depth or not isinstance(fig_dict, dict):
+        return fig_dict
     
-    for key, value in data.items():
+    for key, value in fig_dict.items():
         if key == "title" and isinstance(value, str):
-            data[key] = {"text": value}
+            fig_dict[key] = {"text": value}
         elif isinstance(value, dict):  # Nested dictionary
-            data[key] = update_title_field(value, depth + 1, max_depth)
+            fig_dict[key] = update_title_field(value, depth + 1, max_depth)
         elif isinstance(value, list):  # Lists can contain nested dictionaries
-            data[key] = [update_title_field(item, depth + 1, max_depth) if isinstance(item, dict) else item for item in value]
-    
-    return data
+            fig_dict[key] = [update_title_field(item, depth + 1, max_depth) if isinstance(item, dict) else item for item in value]
+    return fig_dict
+
+
+
+
 
-def remove_extra_information_field(data, depth=1, max_depth=10):
+def convert_to_3d_layout(layout):
+    import copy
+    # Create a deep copy to avoid modifying the original layout
+    new_layout = copy.deepcopy(layout)
+
+    # Add the axis fields inside `scene` first
+    new_layout["scene"] = {
+        "xaxis": layout.get("xaxis", {}),
+        "yaxis": layout.get("yaxis", {}),
+        "zaxis": layout.get("zaxis", {})
+    }
+
+    # Remove the original axis fields from the top-level layout
+    new_layout.pop("xaxis", None)
+    new_layout.pop("yaxis", None)
+    new_layout.pop("zaxis", None)
+
+    return new_layout
+
+    #A bubble plot uses z data, but that data is then
+    #moved into the size field and the z field must be removed.
+def remove_bubble_fields(fig_dict):
+    #This code will modify the data_series inside the fig_dict, directly.
+    bubble_found = False #initialize with false case.
+    for data_series in fig_dict["data"]:
+        if "trace_style" in data_series:
+            if (data_series["trace_style"] == "bubble") or ("max_bubble_size" in data_series):
+                bubble_found = True
+            if bubble_found == True:
+                if "z" in data_series:
+                    data_series.pop("z")
+                if "z_points" in data_series:
+                    data_series.pop("z_points")
+                if "max_bubble_size" in data_series:
+                    data_series.pop("max_bubble_size")
+    if bubble_found == True:
+        if "zaxis" in fig_dict["layout"]:
+            fig_dict["layout"].pop("zaxis")
+    return fig_dict
+
+def update_3d_axes(fig_dict):
+    if "zaxis" in fig_dict["layout"]:
+        fig_dict['layout'] = convert_to_3d_layout(fig_dict['layout'])
+        for data_series_index, data_series in enumerate(fig_dict["data"]):
+            if data_series["type"] == "scatter3d":
+                if "z_matrix" in data_series: #for this one, we don't want the z_matrix.
+                    data_series.pop("z_matrix")
+            if data_series["type"] == "mesh3d":
+                if "z_matrix" in data_series: #for this one, we don't want the z_matrix.
+                    data_series.pop("z_matrix")
+            if data_series["type"] == "surface":
+                if "z_matrix" in data_series: #for this one, we want the z_matrix so we pop z if we have the z_matrix..
+                    data_series.pop("z")
+                print(" The Surface type of 3D plot has not been implemented yet. It requires replacing z with the z_matrix after the equation has been evaluated.")
+    return fig_dict
+
+def remove_extra_information_field(fig_dict, depth=1, max_depth=10):
     """ This function is intended to make JSONGrapher .json files compatible with the current plotly format expectations
-     and also necessary for being able to convert a JSONGRapher json_dict to python plotly figure objects. """
-    """Recursively checks for 'extraInformation' fields and removes them."""
-    if depth > max_depth or not isinstance(data, dict):
-        return data
+     and also necessary for being able to convert a JSONGrapher json_dict to python plotly figure objects.
+    Recursively checks for 'extraInformation' fields and removes them."""
+    if depth > max_depth or not isinstance(fig_dict, dict):
+        return fig_dict
 
     # Use a copy of the dictionary keys to safely modify the dictionary during iteration
-    for key in list(data.keys()):
+    for key in list(fig_dict.keys()):
         if key == ("extraInformation" or "extra_information"):
-            del data[key]  # Remove the field
-        elif isinstance(data[key], dict):  # Nested dictionary
-            data[key] = remove_extra_information_field(data[key], depth + 1, max_depth)
-        elif isinstance(data[key], list):  # Lists can contain nested dictionaries
-            data[key] = [
-                remove_extra_information_field(item, depth + 1, max_depth) if isinstance(item, dict) else item for item in data[key]
+            del fig_dict[key]  # Remove the field
+        elif isinstance(fig_dict[key], dict):  # Nested dictionary
+            fig_dict[key] = remove_extra_information_field(fig_dict[key], depth + 1, max_depth)
+        elif isinstance(fig_dict[key], list):  # Lists can contain nested dictionaries
+            fig_dict[key] = [
+                remove_extra_information_field(item, depth + 1, max_depth) if isinstance(item, dict) else item for item in fig_dict[key]
             ]
     
-    return data
+    return fig_dict
     
 
 def remove_nested_comments(data, top_level=True):
     """ This function is intended to make JSONGrapher .json files compatible with the current plotly format expectations
-     and also necessary for being able to convert a JSONGRapher json_dict to python plotly figure objects. """
-    """Removes 'comments' fields that are not at the top level of the JSON-dict. Starts with 'top_level = True' when dict is first passed in then becomes false after that. """
+     and also necessary for being able to convert a JSONGrapher json_dict to python plotly figure objects. 
+    Removes 'comments' fields that are not at the top level of the JSON-dict. Starts with 'top_level = True' when dict is first passed in then becomes false after that. """
     if not isinstance(data, dict):
         return data
     # Process nested structures
@@ -1470,18 +3050,47 @@ def remove_simulate_field(json_fig_dict):
     json_fig_dict['data'] = data_dicts_list #this line shouldn't be necessary, but including it for clarity and carefulness.
     return json_fig_dict
 
-def remove_custom_units_chevrons(json_fig_dict):
-    json_fig_dict['layout']['xaxis']['title']['text'] = json_fig_dict['layout']['xaxis']['title']['text'].replace('<','').replace('>','')
-    json_fig_dict['layout']['yaxis']['title']['text'] = json_fig_dict['layout']['yaxis']['title']['text'].replace('<','').replace('>','')
+def remove_equation_field(json_fig_dict):
+    data_dicts_list = json_fig_dict['data']
+    for data_dict in data_dicts_list:
+        data_dict.pop('equation', None) #Some people recommend using pop over if/del as safer. Both ways should work under normal circumstances.
+    json_fig_dict['data'] = data_dicts_list #this line shouldn't be necessary, but including it for clarity and carefulness.
     return json_fig_dict
 
+def remove_trace_style_field(json_fig_dict):
+    data_dicts_list = json_fig_dict['data']
+    for data_dict in data_dicts_list:
+        data_dict.pop('trace_style', None) #Some people recommend using pop over if/del as safer. Both ways should work under normal circumstances.
+        data_dict.pop('tracetype', None) #Some people recommend using pop over if/del as safer. Both ways should work under normal circumstances.
+    json_fig_dict['data'] = data_dicts_list #this line shouldn't be necessary, but including it for clarity and carefulness.
+    return json_fig_dict
 
-def clean_json_fig_dict(json_fig_dict, fields_to_update=["title_field", "extraInformation", "nested_comments"]):
+def remove_custom_units_chevrons(json_fig_dict):
+    try:
+        json_fig_dict['layout']['xaxis']['title']['text'] = json_fig_dict['layout']['xaxis']['title']['text'].replace('<','').replace('>','')
+    except KeyError:
+        pass
+    try:
+        json_fig_dict['layout']['yaxis']['title']['text'] = json_fig_dict['layout']['yaxis']['title']['text'].replace('<','').replace('>','')
+    except KeyError:
+        pass
+    try:
+        json_fig_dict['layout']['zaxis']['title']['text'] = json_fig_dict['layout']['zaxis']['title']['text'].replace('<','').replace('>','')
+    except KeyError:
+        pass
+    return json_fig_dict
+
+def clean_json_fig_dict(json_fig_dict, fields_to_update=None):
     """ This function is intended to make JSONGrapher .json files compatible with the current plotly format expectations
-     and also necessary for being able to convert a JSONGRapher json_dict to python plotly figure objects. 
+     and also necessary for being able to convert a JSONGrapher json_dict to python plotly figure objects. 
+     fields_to_update should be a list.
      This function can also remove the 'simulate' field from data series. However, that is not the default behavior
      because one would not want to do that by mistake before simulation is performed.
+     This function can also remove the 'equation' field from data series. However, that is not the default behavior
+     because one would not want to do that by mistake before the equation is evaluated.
      """
+    if fields_to_update is None:  # should not initialize mutable objects in arguments line, so doing here.
+        fields_to_update = ["title_field", "extraInformation", "nested_comments"]
     fig_dict = json_fig_dict
     #unmodified_data = copy.deepcopy(data)
     if "title_field" in fields_to_update:
@@ -1492,14 +3101,22 @@ def clean_json_fig_dict(json_fig_dict, fields_to_update=["title_field", "extraIn
         fig_dict = remove_nested_comments(fig_dict)
     if "simulate" in fields_to_update:
         fig_dict = remove_simulate_field(fig_dict)
+    if "equation" in fields_to_update:
+        fig_dict = remove_equation_field(fig_dict)
     if "custom_units_chevrons" in fields_to_update:
         fig_dict = remove_custom_units_chevrons(fig_dict)
+    if "bubble" in fields_to_update: #must be updated before trace_style is removed.
+        fig_dict = remove_bubble_fields(fig_dict)
+    if "trace_style" in fields_to_update:
+        fig_dict = remove_trace_style_field(fig_dict)
+    if "3d_axes" in fields_to_update: #This is for 3D plots
+        fig_dict = update_3d_axes(fig_dict)
 
     return fig_dict
 
 ### End section of code with functions for cleaning fig_dicts for plotly compatibility ###
 
-### Beginning of section of file that has functions for calling external javascript simulators ###
+### Beginning of section of file that has functions for "simulate" and "equation" fields, to evaluate equations and call external javascript simulators, as well as support functions ###
 
 def run_js_simulation(javascript_simulator_url, simulator_input_json_dict, verbose = False):
     """
@@ -1527,7 +3144,7 @@ def run_js_simulation(javascript_simulator_url, simulator_input_json_dict, verbo
     """
     import requests
     import subprocess
-    import json
+    #import json
     import os
 
     # Convert to raw GitHub URL only if "raw" is not in the original URL
@@ -1542,14 +3159,14 @@ def run_js_simulation(javascript_simulator_url, simulator_input_json_dict, verbo
     js_filename = os.path.basename(javascript_simulator_url)
 
     # Download the JavaScript file
-    response = requests.get(javascript_simulator_url)
+    response = requests.get(javascript_simulator_url, timeout=300)
 
     if response.status_code == 200:
-        with open(js_filename, "w") as file:
+        with open(js_filename, "w", encoding="utf-8") as file:  # Specify UTF-8 encoding for compatibility
             file.write(response.text)
 
         # Append the export statement to the JavaScript file
-        with open(js_filename, "a") as file:
+        with open(js_filename, "a", encoding="utf-8") as file:  # Specify UTF-8 encoding for compatibility
             file.write("\nmodule.exports = { simulate };")
 
         # Convert input dictionary to a JSON string
@@ -1561,7 +3178,7 @@ def run_js_simulation(javascript_simulator_url, simulator_input_json_dict, verbo
         console.log(JSON.stringify(simulator.simulate({input_json_str})));
         """
 
-        result = subprocess.run(["node", "-e", js_command], capture_output=True, text=True)
+        result = subprocess.run(["node", "-e", js_command], capture_output=True, text=True, check=True)
 
         # Print output and errors if verbose
         if verbose:
@@ -1612,55 +3229,267 @@ def convert_to_raw_github_url(url):
 #This function takes in a data_series_dict object and then
 #calls an external javascript simulation if needed
 #Then fills the data_series dict with the simulated data.
+#This function is not intended to be called by the regular user
+#because it returns extra fields that need to be parsed out.
+#and because it does not do unit conversions as needed after the simulation resultss are returned.
 def simulate_data_series(data_series_dict, simulator_link='', verbose=False):
     if simulator_link == '':
-        simulator_link = data_series_dict["simulate"]["model"]
-    #need to provide the link and the data_dict
-    simulation_return = run_js_simulation(simulator_link, data_series_dict, verbose = verbose)
-    data_series_dict_filled = simulation_return["data"]
-    return data_series_dict_filled
+        simulator_link = data_series_dict["simulate"]["model"]  
+    try:
+        simulation_return = run_js_simulation(simulator_link, data_series_dict, verbose=verbose)
+        if isinstance(simulation_return, dict) and "error" in simulation_return: # Check for errors in the returned data
+            print(f"Simulation failed: {simulation_return.get('error_message', 'Unknown error')}")
+            print(simulation_return)
+            return None
+        return simulation_return.get("data", None)
+
+    except Exception as e: # This is so VS code pylint does not flag this line. pylint: disable=broad-except
+        print(f"Exception occurred in simulate_data_series function of JSONRecordCreator.py: {e}")
+        return None
 
 #Function that goes through a fig_dict data series and simulates each data series as needed.
-#could probably change this into a loop that calls simulate_specific_data_series_by_index
 #If the simulated data returned has "x_label" and/or "y_label" with units, those will be used to scale the data, then will be removed.
 def simulate_as_needed_in_fig_dict(fig_dict, simulator_link='', verbose=False):
+    data_dicts_list = fig_dict['data']    
+    for data_dict_index in range(len(data_dicts_list)):
+        fig_dict = simulate_specific_data_series_by_index(fig_dict, data_dict_index, simulator_link=simulator_link, verbose=verbose)
+    return fig_dict
+
+#Function that takes fig_dict and dataseries index and simulates if needed. Also performs unit conversions as needed.
+#If the simulated data returned has "x_label" and/or "y_label" with units, those will be used to scale the data, then will be removed.
+def simulate_specific_data_series_by_index(fig_dict, data_series_index, simulator_link='', verbose=False):
+    data_dicts_list = fig_dict['data']
+    data_dict_index = data_series_index
+    data_dict = data_dicts_list[data_dict_index]
+    if 'simulate' in data_dict:
+        data_dict_filled = simulate_data_series(data_dict, simulator_link=simulator_link, verbose=verbose)
+        # Check if unit scaling is needed
+        if ("x_label" in data_dict_filled) or ("y_label" in data_dict_filled):
+            #first, get the units that are in the layout of fig_dict so we know what to convert to.
+            existing_record_x_label = fig_dict["layout"]["xaxis"]["title"]["text"]
+            existing_record_y_label = fig_dict["layout"]["yaxis"]["title"]["text"]
+            # Extract units  from the simulation output.
+            existing_record_x_units = separate_label_text_from_units(existing_record_x_label).get("units", "")
+            existing_record_y_units = separate_label_text_from_units(existing_record_y_label).get("units", "")
+            simulated_data_series_x_units = separate_label_text_from_units(data_dict_filled.get('x_label', '')).get("units", "")
+            simulated_data_series_y_units = separate_label_text_from_units(data_dict_filled.get('y_label', '')).get("units", "")
+            # Compute unit scaling ratios
+            x_units_ratio = get_units_scaling_ratio(simulated_data_series_x_units, existing_record_x_units) if simulated_data_series_x_units and existing_record_x_units else 1
+            y_units_ratio = get_units_scaling_ratio(simulated_data_series_y_units, existing_record_y_units) if simulated_data_series_y_units and existing_record_y_units else 1
+            # Apply scaling to the data series
+            scale_dataseries_dict(data_dict_filled, num_to_scale_x_values_by=x_units_ratio, num_to_scale_y_values_by=y_units_ratio)
+            #Verbose logging for debugging
+            if verbose:
+                print(f"Scaling X values by: {x_units_ratio}, Scaling Y values by: {y_units_ratio}")
+            #Now need to remove the "x_label" and "y_label" to be compatible with plotly.
+            data_dict_filled.pop("x_label", None)
+            data_dict_filled.pop("y_label", None)
+        # Update the figure dictionary
+        data_dicts_list[data_dict_index] = data_dict_filled
+    fig_dict['data'] = data_dicts_list
+    return fig_dict
+
+def evaluate_equations_as_needed_in_fig_dict(fig_dict):
     data_dicts_list = fig_dict['data']
     for data_dict_index, data_dict in enumerate(data_dicts_list):
-        if 'simulate' in data_dict:
-            data_dict_filled = simulate_data_series(data_dict, simulator_link=simulator_link, verbose=verbose)
-            #data_dict_filled may include "x_label" and/or "y_label". If it does, we'll need to check about scaling units.
-            if (("x_label" in data_dict_filled) or ("y_label" in data_dict_filled)):
-                #first, get the units that are in the layout of fig_dict so we know what to convert to.
-                existing_record_x_label = fig_dict["layout"]["xaxis"]["title"]["text"] #this is a dictionary.
-                existing_record_y_label = fig_dict["layout"]["yaxis"]["title"]["text"] #this is a dictionary.
-                existing_record_x_units = separate_label_text_from_units(existing_record_x_label)["units"]
-                existing_record_y_units = separate_label_text_from_units(existing_record_y_label)["units"]
-                #now, get the units from the simulation output.
+        if 'equation' in data_dict:
+            fig_dict = evaluate_equation_for_data_series_by_index(fig_dict, data_dict_index)
+    return fig_dict
+
+#TODO: Should add z units ratio scaling here (just to change units when merging records). Should do the same for the simulate_specific_data_series_by_index function.
+def evaluate_equation_for_data_series_by_index(fig_dict, data_series_index, verbose="auto"):   
+    try:
+        # Attempt to import from the json_equationer package
+        import json_equationer.equation_creator as equation_creator
+    except ImportError:
+        try:
+             # Fallback: attempt local import
+            from . import equation_creator
+        except ImportError as exc:
+             # Log the failure and handle gracefully
+            print(f"Failed to import equation_creator: {exc}")
+    import copy
+    data_dicts_list = fig_dict['data']
+    data_dict = data_dicts_list[data_series_index]
+    if 'equation' in data_dict:
+        equation_object = equation_creator.Equation(data_dict['equation'])
+        if verbose == "auto":
+            equation_dict_evaluated = equation_object.evaluate_equation()
+        else:
+            equation_dict_evaluated = equation_object.evaluate_equation(verbose=verbose)
+        if "graphical_dimensionality" in equation_dict_evaluated:
+            graphical_dimensionality = equation_dict_evaluated["graphical_dimensionality"]
+        else:
+            graphical_dimensionality = 2
+        data_dict_filled = copy.deepcopy(data_dict)
+        data_dict_filled['equation'] = equation_dict_evaluated
+        data_dict_filled['x_label'] = data_dict_filled['equation']['x_variable'] 
+        data_dict_filled['y_label'] = data_dict_filled['equation']['y_variable'] 
+        data_dict_filled['x'] = equation_dict_evaluated['x_points']
+        data_dict_filled['y'] = equation_dict_evaluated['y_points']
+        if graphical_dimensionality == 3:
+            data_dict_filled['z_label'] = data_dict_filled['equation']['z_variable'] 
+            data_dict_filled['z'] = equation_dict_evaluated['z_points']
+        #data_dict_filled may include "x_label" and/or "y_label". If it does, we'll need to check about scaling units.
+        if (("x_label" in data_dict_filled) or ("y_label" in data_dict_filled)) or ("z_label" in data_dict_filled):
+            #first, get the units that are in the layout of fig_dict so we know what to convert to.
+            existing_record_x_label = fig_dict["layout"]["xaxis"]["title"]["text"] #this is a dictionary.
+            existing_record_y_label = fig_dict["layout"]["yaxis"]["title"]["text"] #this is a dictionary.
+            existing_record_x_units = separate_label_text_from_units(existing_record_x_label)["units"]
+            existing_record_y_units = separate_label_text_from_units(existing_record_y_label)["units"]
+            if "z_label" in data_dict_filled:
+                existing_record_z_label = fig_dict["layout"]["zaxis"]["title"]["text"] #this is a dictionary.
+            if (existing_record_x_units == '') and (existing_record_y_units == ''): #skip scaling if there are no units.
+                pass
+            else: #If we will be scaling...
+                #now, get the units from the evaluated equation output.
                 simulated_data_series_x_units = separate_label_text_from_units(data_dict_filled['x_label'])["units"]
                 simulated_data_series_y_units = separate_label_text_from_units(data_dict_filled['y_label'])["units"]
                 x_units_ratio = get_units_scaling_ratio(simulated_data_series_x_units, existing_record_x_units)
                 y_units_ratio = get_units_scaling_ratio(simulated_data_series_y_units, existing_record_y_units)
                 #We scale the dataseries, which really should be a function.
                 scale_dataseries_dict(data_dict_filled, num_to_scale_x_values_by = x_units_ratio, num_to_scale_y_values_by = y_units_ratio)
-                #Now need to remove the "x_label" and "y_label" to be compatible with plotly.
-                data_dict_filled.pop("x_label", None)
-                data_dict_filled.pop("y_label", None)
-            data_dicts_list[data_dict_index] = data_dict_filled
+            #Now need to remove the "x_label" and "y_label" to be compatible with plotly.
+            data_dict_filled.pop("x_label", None)
+            data_dict_filled.pop("y_label", None)
+            if "z_label" in data_dict_filled:
+                data_dict_filled.pop("z_label", None)
+        if "type" not in data_dict:
+            if graphical_dimensionality == 2:
+                data_dict_filled['type'] = 'spline'
+            elif graphical_dimensionality == 3:
+                data_dict_filled['type'] = 'mesh3d'
+        data_dicts_list[data_series_index] = data_dict_filled
     fig_dict['data'] = data_dicts_list
     return fig_dict
 
-#Function that takes fig_dict and dataseries index and simulates if needed.
-def simulate_specific_data_series_by_index(fig_dict, data_series_index, simulator_link='', verbose=False):
-    data_dicts_list = fig_dict['data']
-    data_dict_index = data_series_index
-    data_dict = data_dicts_list[data_dict_index]
-    if 'simulate' in data_dict:
-        data_dict_filled = simulate_data_series(data_dict, simulator_link=simulator_link, verbose=verbose)
-        data_dicts_list[data_dict_index] = data_dict_filled
-    fig_dict['data'] = data_dicts_list
+
+def update_implicit_data_series_data(target_fig_dict, source_fig_dict, parallel_structure=True, modify_target_directly = False):
+    """
+    Updates the x and y values of implicit data series (equation/simulate) in target_fig_dict 
+    using values from the corresponding series in source_fig_dict.
+
+    Args:
+        target_fig_dict (dict): The figure dictionary that needs updated data.
+        source_fig_dict (dict): The figure dictionary that provides x and y values.
+        parallel_structure (bool, optional): If True, assumes both data lists are the same 
+                                             length and updates using zip(). If False, 
+                                             matches by name instead. Default is True.
+
+    Returns:
+        dict: A new figure dictionary with updated x and y values for implicit data series.
+
+    Notes:
+        - If parallel_structure=True and both lists have the same length, updates use zip().
+        - If parallel_structure=False, matching is done by the "name" field.
+        - Only updates data series that contain "simulate" or "equation".
+        - Ensures deep copying to avoid modifying the original structures.
+    """
+    if modify_target_directly == False:
+        import copy  # Import inside function to limit scope   
+        updated_fig_dict =  copy.deepcopy(target_fig_dict)  # Deep copy to avoid modifying original
+    else:
+        updated_fig_dict = target_fig_dict
+
+    target_data_series = updated_fig_dict.get("data", [])
+    source_data_series = source_fig_dict.get("data", [])
+
+    if parallel_structure and len(target_data_series) == len(source_data_series):
+        # Use zip() when parallel_structure=True and lengths match
+        for target_series, source_series in zip(target_data_series, source_data_series):
+            if ("equation" in target_series) or ("simulate" in target_series):
+                target_series["x"] = source_series.get("x", [])  # Extract and apply "x" values
+                target_series["y"] = source_series.get("y", [])  # Extract and apply "y" values
+                if "z" in source_series:
+                    target_series["z"] = source_series.get("z", [])  # Extract and apply "z" values                    
+    else:
+        # Match by name when parallel_structure=False or lengths differ
+        source_data_dict = {series["name"]: series for series in source_data_series if "name" in series}
+
+        for target_series in target_data_series:
+            if ("equation" in target_series) or ("simulate" in target_series):
+                target_name = target_series.get("name")
+               
+                if target_name in source_data_dict:
+                    source_series = source_data_dict[target_name]
+                    target_series["x"] = source_series.get("x", [])  # Extract and apply "x" values
+                    target_series["y"] = source_series.get("y", [])  # Extract and apply "y" values
+                    if "z" in source_series:
+                        target_series["z"] = source_series.get("z", [])  # Extract and apply "z" values                    
+    return updated_fig_dict
+
+
+def execute_implicit_data_series_operations(fig_dict, simulate_all_series=True, evaluate_all_equations=True, adjust_implicit_data_ranges=True):
+    """
+    This function is designed to be called during creation of a plotly or matplotlib figure creation.
+    Processes implicit data series (equation/simulate), adjusting ranges, performing simulations,
+    and evaluating equations as needed.
+
+    The important thing is that this function creates a "fresh" fig_dict, does some manipulation, then then gets the data from that
+    and adds it to the original fig_dict.
+    That way the original fig_dict is not changed other than getting the simulated/evaluated data.
+
+    The reason the function works this way is that the x_range_default of the implicit data series (equations and simulations)
+    are adjusted to match the data in the fig_dict, but we don't want to change the x_range_default of our main record.
+    That's why we make a copy for creating simulated/evaluated data from those adjusted ranges, and then put the simulated/evaluated data
+    back into the original dict.
+
+    
+
+    Args:
+        fig_dict (dict): The figure dictionary containing data series.
+        simulate_all_series (bool): If True, performs simulations for applicable series.
+        evaluate_all_equations (bool): If True, evaluates all equation-based series.
+        adjust_implicit_data_ranges (bool): If True, modifies ranges for implicit data series.
+
+    Returns:
+        dict: Updated figure dictionary with processed implicit data series.
+
+    Notes:
+        - If adjust_implicit_data_ranges=True, retrieves min/max values from regular data series 
+          (those that are not equations and not simulations) and applies them to implicit data.
+        - If simulate_all_series=True, executes simulations for all series that require them 
+          and transfers the computed data back to fig_dict without copying ranges.
+        - If evaluate_all_equations=True, solves equations as needed and transfers results 
+          back to fig_dict without copying ranges.
+        - Uses deepcopy to avoid modifying the original input dictionary.
+    """
+    import copy  # Import inside function for modularity
+
+    # Create a copy for processing implicit series separately
+    fig_dict_for_implicit = copy.deepcopy(fig_dict)
+    #first check if any data_series have an equatinon or simulation field. If not, we'll skip.
+    #initialize with false:
+    implicit_series_present = False
+
+    for data_series in fig_dict["data"]:
+        if ("equation" in data_series) or ("simulate" in data_series):
+            implicit_series_present = True
+    if implicit_series_present == True:
+        if adjust_implicit_data_ranges:
+            # Retrieve ranges from data series that are not equation-based or simulation-based.
+            fig_dict_ranges, data_series_ranges = get_fig_dict_ranges(fig_dict, skip_equations=True, skip_simulations=True)
+            data_series_ranges # Variable not used. The remainder of this comment is to avoid vs code pylint flagging. pylint: disable=pointless-statement
+            # Apply the extracted ranges to implicit data series before simulation or equation evaluation.
+            fig_dict_for_implicit = update_implicit_data_series_x_ranges(fig_dict, fig_dict_ranges)
+
+        if simulate_all_series:
+            # Perform simulations for applicable series
+            fig_dict_for_implicit = simulate_as_needed_in_fig_dict(fig_dict_for_implicit)
+            # Copy data back to fig_dict, ensuring ranges remain unchanged
+            fig_dict = update_implicit_data_series_data(target_fig_dict=fig_dict, source_fig_dict=fig_dict_for_implicit, parallel_structure=True, modify_target_directly=True)
+
+        if evaluate_all_equations:
+            # Evaluate equations that require computation
+            fig_dict_for_implicit = evaluate_equations_as_needed_in_fig_dict(fig_dict_for_implicit)
+            # Copy results back without overwriting the ranges
+            fig_dict = update_implicit_data_series_data(target_fig_dict=fig_dict, source_fig_dict=fig_dict_for_implicit, parallel_structure=True, modify_target_directly=True)
+
     return fig_dict
 
-### End of section of file that has functions for calling external javascript simulators ###
+
+
+### End of section of file that has functions for "simulate" and "equation" fields, to evaluate equations and call external javascript simulators, as well as support functions###
 
 # Example Usage
 if __name__ == "__main__":
@@ -1669,7 +3498,7 @@ if __name__ == "__main__":
         comments="Here is a description.",
         graph_title="Here Is The Graph Title Spot",
         data_objects_list=[
-            {"comments": "Initial data series.", "uid": "123", "name": "Series A", "type": "spline", "x": [1, 2, 3], "y": [4, 5, 8]}
+            {"comments": "Initial data series.", "uid": "123", "name": "Series A", "trace_style": "spline", "x": [1, 2, 3], "y": [4, 5, 8]}
         ],
     )
     x_label_including_units= "Time (years)" 
@@ -1685,14 +3514,14 @@ if __name__ == "__main__":
     print(Record)
 
     # Example of creating a record from an existing dictionary.
-    existing_JSONGrapher_record = {
+    example_existing_JSONGrapher_record = {
         "comments": "Existing record description.",
         "graph_title": "Existing Graph",
         "data": [
             {"comments": "Data series 1", "uid": "123", "name": "Series A", "type": "spline", "x": [1, 2, 3], "y": [4, 5, 8]}
         ],
     }
-    Record_from_existing = JSONGrapherRecord(existing_JSONGrapher_record=existing_JSONGrapher_record)
+    Record_from_existing = JSONGrapherRecord(existing_JSONGrapher_record=example_existing_JSONGrapher_record)
     x_label_including_units= "Time (years)" 
     y_label_including_units = "Height (cm)"
     Record_from_existing.set_comments("Tree Growth Data collected from the US National Arboretum")
@@ -1701,7 +3530,8 @@ if __name__ == "__main__":
     Record_from_existing.set_y_axis_label_including_units(y_label_including_units)
     print(Record_from_existing)
     
-    print("NOW WILL MERGE THE RECORDS, AND USE THE SECOND ONE TWICE (AS A JSONGRAPHER OBJECT THEN JUST THE FIG_DICT)")
+    print("NOW WILL MERGE THE RECORDS, AND USE THE SECOND ONE TWICE (AS A JSONGrapher OBJECT THEN JUST THE FIG_DICT)")
     print(merge_JSONGrapherRecords([Record, Record_from_existing, Record_from_existing.fig_dict]))
 
 
+