spacr 0.4.0__py3-none-any.whl → 0.4.2__py3-none-any.whl

spacr/utils.py

@@ -319,7 +319,6 @@ def load_settings(csv_file_path, show=False, setting_key='setting_key', setting_
 
     return result_dict
 
-
 def save_settings(settings, name='settings', show=False):
     
     settings_df = pd.DataFrame(list(settings.items()), columns=['Key', 'Value'])
@@ -328,14 +327,19 @@ def save_settings(settings, name='settings', show=False):
     
     if isinstance(settings['src'], list):
         src = settings['src'][0]
-        #if os.path.exists(src):
-
         name = f"{name}_list"
     else:
         src = settings['src']
+        
+    if 'test_mode' in settings.keys():
+        settings['test_mode'] = False
+        
+        if 'plot' in settings.keys():
+            settings['plot'] = False
 
     settings_csv = os.path.join(src,'settings',f'{name}.csv')
     os.makedirs(os.path.join(src,'settings'), exist_ok=True)
+    print(f"Saving settings to {settings_csv}")
     settings_df.to_csv(settings_csv, index=False)
 
 def print_progress(files_processed, files_to_process, n_jobs, time_ls=None, batch_size=None, operation_type=""):
@@ -1145,7 +1149,7 @@ def _masks_to_masks_stack(masks):
         mask_stack.append(mask)
     return mask_stack
     
-def _get_diam(mag, obj):
+def _get_diam_v1(mag, obj):
 
     if mag == 20:
         if obj == 'cell':
@@ -1176,11 +1180,28 @@ def _get_diam(mag, obj):
             diamiter = 60
         else:
             raise ValueError("Invalid magnification: Use 20, 40 or 60")
+
     else:
         raise ValueError("Invalid magnification: Use 20, 40 or 60")
     
     return diamiter
 
+def _get_diam(mag, obj):
+
+    if obj == 'cell':
+        diamiter = 2 * mag + 80
+        
+    if obj == 'cell_large':
+        diamiter = 2 * mag + 120
+                                
+    if obj == 'nucleus':
+        diamiter = 0.75 * mag + 45
+                                
+    if obj == 'pathogen':
+        diamiter = mag
+                                
+    return int(diamiter)
+
 def _get_object_settings(object_type, settings):
     object_settings = {}
 
@@ -1333,20 +1354,25 @@ def annotate_conditions(df, cells=None, cell_loc=None, pathogens=None, pathogen_
     def _map_or_default(column_name, values, loc, df):
         """
         Consolidates the logic for mapping values or assigning defaults when loc is None.
-
+    
         Args:
             column_name (str): The column in the DataFrame to annotate.
             values (list/str): The list of values or a single string to annotate.
             loc (list of lists): Location mapping for the values, or None if not used.
             df (pandas.DataFrame): The DataFrame to modify.
         """
-        if isinstance(values, str) or (isinstance(values, list) and loc is None):
-            # Assign all rows the first value in the list or the single string
-            df[column_name] = values if isinstance(values, str) else values[0]
+        if isinstance(values, str) and loc is None:
+            # If a single string is provided and loc is None, assign the value to all rows
+            df[column_name] = values  
+    
+        elif isinstance(values, list) and loc is None:
+            # If a list of values is provided but no loc, assign the first value to all rows
+            df[column_name] = values[0]
+    
         elif values is not None and loc is not None:
-            # Perform the location-based mapping
+            # Perform location-based mapping
             value_dict = {val: key for key, loc_list in zip(values, loc) for val in loc_list}
-            df[column_name] = np.nan
+            df[column_name] = np.nan  # Start with NaN
             for val, key in value_dict.items():
                 loc_type = _get_type(val)
                 if loc_type:
@@ -3099,12 +3125,8 @@ def _get_regex(metadata_type, img_format, custom_regex=None):
         regex = f'(?P<plateID>.*)_(?P<wellID>.*)_T(?P<timeID>.*)F(?P<fieldID>.*)L(?P<laserID>..)A(?P<AID>..)Z(?P<sliceID>.*)C(?P<chanID>.*){img_format}'
     elif metadata_type == 'cq1':
         regex = f'W(?P<wellID>.*)F(?P<fieldID>.*)T(?P<timeID>.*)Z(?P<sliceID>.*)C(?P<chanID>.*){img_format}'
-    elif metadata_type == 'nikon':
-        regex = f'(?P<plateID>.*)_(?P<wellID>.*)_T(?P<timeID>.*)F(?P<fieldID>.*)L(?P<laserID>..)A(?P<AID>..)Z(?P<sliceID>.*)C(?P<chanID>.*){img_format}'
-    elif metadata_type == 'zeis':
-        regex = f'(?P<plateID>.*)_(?P<wellID>.*)_T(?P<timeID>.*)F(?P<fieldID>.*)L(?P<laserID>..)A(?P<AID>..)Z(?P<sliceID>.*)C(?P<chanID>.*){img_format}'
-    elif metadata_type == 'leica':
-        regex = f'(?P<plateID>.*)_(?P<wellID>.*)_T(?P<timeID>.*)F(?P<fieldID>.*)L(?P<laserID>..)A(?P<AID>..)Z(?P<sliceID>.*)C(?P<chanID>.*){img_format}'
+    elif metadata_type == 'auto':
+        regex = f'(?P<plateID>.*)_(?P<wellID>.*)_T(?P<timeID>.*)F(?P<fieldID>.*)L(?P<laserID>.*)C(?P<chanID>.*).tif'     
     elif metadata_type == 'custom':
         regex = f'({custom_regex}){img_format}'
         
@@ -4945,7 +4967,7 @@ def download_models(repo_id="einarolafsson/models", retries=5, delay=5):
     if not os.path.exists(local_dir):
         os.makedirs(local_dir)
     elif len(os.listdir(local_dir)) > 0:
-        print(f"Models already downloaded to: {local_dir}")
+        #print(f"Models already downloaded to: {local_dir}")
         return local_dir
 
     attempt = 0
@@ -5011,22 +5033,22 @@ def generate_cytoplasm_mask(nucleus_mask, cell_mask):
     return cytoplasm_mask
 
 def add_column_to_database(settings):
-    #"""
-    #Adds a new column to the database table by matching on a common column from the DataFrame.
-    #If the column already exists in the database, it adds the column with a suffix.
-    #NaN values will remain as NULL in the database.
-
-    #Parameters:
-    #    settings (dict): A dictionary containing the following keys:
-    #    csv_path (str): Path to the CSV file with the data to be added.
-    #    db_path (str): Path to the SQLite database (or connection string for other databases).
-    #    table_name (str): The name of the table in the database.
-    #    update_column (str): The name of the new column in the DataFrame to add to the database.
-    #    match_column (str): The common column used to match rows.
-
-    #Returns:
-    #    None
-    #"""
+    """
+    Adds a new column to the database table by matching on a common column from the DataFrame.
+    If the column already exists in the database, it adds the column with a suffix.
+    NaN values will remain as NULL in the database.
+
+    Parameters:
+        settings (dict): A dictionary containing the following keys:
+            csv_path (str): Path to the CSV file with the data to be added.
+            db_path (str): Path to the SQLite database (or connection string for other databases).
+            table_name (str): The name of the table in the database.
+            update_column (str): The name of the new column in the DataFrame to add to the database.
+            match_column (str): The common column used to match rows.
+
+    Returns:
+        None
+    """
 
     # Read the DataFrame from the provided CSV path
     df = pd.read_csv(settings['csv_path'])
@@ -5337,3 +5359,63 @@ def calculate_shortest_distance(df, object1, object2):
     df[f'{object1}_{object2}_shortest_distance'] = np.maximum(shortest_distance, 0)
 
     return df
+
+def format_path_for_system(path):
+    """
+    Takes a file path and reformats it to be compatible with the current operating system.
+    
+    Args:
+        path (str): The file path to be formatted.
+
+    Returns:
+        str: The formatted path for the current operating system.
+    """
+    system = platform.system()
+    
+    # Convert Windows-style paths to Unix-style (Linux/macOS)
+    if system in ["Linux", "Darwin"]:  # Darwin is macOS
+        formatted_path = path.replace("\\", "/")
+    
+    # Convert Unix-style paths to Windows-style
+    elif system == "Windows":
+        formatted_path = path.replace("/", "\\")
+    
+    else:
+        raise ValueError(f"Unsupported OS: {system}")
+    
+    # Normalize path to ensure consistency
+    new_path = os.path.normpath(formatted_path)
+    if os.path.exists(new_path):
+        print(f"Found path: {new_path}")
+    else:
+        print(f"Path not found: {new_path}")
+        
+    return new_path
+
+
+def normalize_src_path(src):
+    """
+    Ensures that the 'src' value is properly formatted as either a list of strings or a single string.
+
+    Args:
+        src (str or list): The input source path(s).
+
+    Returns:
+        list or str: A correctly formatted list if the input was a list (or string representation of a list),
+                     otherwise a single string.
+    """
+    if isinstance(src, list):
+        return src  # Already a list, return as-is
+
+    if isinstance(src, str):
+        try:
+            # Check if it is a string representation of a list
+            evaluated_src = ast.literal_eval(src)
+            if isinstance(evaluated_src, list) and all(isinstance(item, str) for item in evaluated_src):
+                return evaluated_src  # Convert to real list
+        except (SyntaxError, ValueError):
+            pass  # Not a valid list, treat as a string
+
+        return src  # Return as a string if not a list
+
+    raise ValueError(f"Invalid type for 'src': {type(src).__name__}, expected str or list")

{spacr-0.4.0.dist-info → spacr-0.4.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.4.0
+Version: 0.4.2
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -41,6 +41,7 @@ Requires-Dist: pillow<11.0,>=10.2.0
 Requires-Dist: tifffile>=2023.4.12
 Requires-Dist: nd2reader<4.0,>=3.3.0
 Requires-Dist: czifile
+Requires-Dist: readlif
 Requires-Dist: imageio<3.0,>=2.34.0
 Requires-Dist: pingouin<1.0,>=0.5.5
 Requires-Dist: umap-learn<1.0,>=0.5.6

{spacr-0.4.0.dist-info → spacr-0.4.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-spacr/__init__.py,sha256=KgkkUyqbm4kh8bwxWeFpp4rilNE0y0RkeylPvS-cTLY,1395
+spacr/__init__.py,sha256=iPlE-WRc1CjSNGPMbVvEKlJsTQlKjq29VjzvNUCpcOM,1401
 spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
 spacr/app_annotate.py,sha256=W9eLPa_LZIvXsXx_-0iDFEU938LBDvRy6prXo0qF4KQ,2533
 spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
@@ -9,27 +9,28 @@ spacr/app_sequencing.py,sha256=DjG26jy4cpddnV8WOOAIiExtOe9MleVMY4MFa5uTo5w,157
 spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
 spacr/cellpose.py,sha256=RBHMs2vwXcfkj0xqAULpALyzJYXddSRycgZSzmwI7v0,14755
 spacr/chat_bot.py,sha256=n3Fhqg3qofVXHmh3H9sUcmfYy9MmgRnr48663MVdY9E,1244
-spacr/core.py,sha256=lKeqmsVrGQ8cPU_WkoNGNBWrk-gtR1RkRkwDdnJ0u64,48829
-spacr/deep_spacr.py,sha256=AsAbehxPChAq65YVPuFqCt5JabdeO8AwVWZmcmyLeFw,58020
+spacr/core.py,sha256=KymF-YPvODMkp4J3xva7NwAKBLAUK_Z5x8_pjl9oaP4,49448
+spacr/deep_spacr.py,sha256=WN64EaQqF87JZg3Uan46t5Y28xsAGD2KMjr2ht6CyDs,54563
 spacr/gui.py,sha256=ARyn9Q_g8HoP-cXh1nzMLVFCKqthY4v2u9yORyaQqQE,8230
-spacr/gui_core.py,sha256=U0A7waKgWq_Es9fMwcZbXUZYGzCqt2bgfY3HbxiFXnw,47466
-spacr/gui_elements.py,sha256=HmITDncklKwtdFhxLhtYXOwndsRfgwWIPVi83VlXHB4,146419
-spacr/gui_utils.py,sha256=0rDF23BUGcmjSJvfCiLoxhlGJdHkio1jTxyCzrMXr-g,41211
-spacr/io.py,sha256=oqJwDJWksVdWE0bRAwytTOsjlL0o-J9lr_pQaw2cQ4Y,138288
+spacr/gui_core.py,sha256=BZpIdNztQn9U2BZxRsmYhr2uhVAm7ZW8-nZxu38QUvs,59027
+spacr/gui_elements.py,sha256=Or38I_X9-lJRsyIAtbEfZPXzls0IORagf7vEe6IlI5Y,152647
+spacr/gui_utils.py,sha256=dWVPFwDj793Z3ERG4mMC0hI0MKkOrvXJpUYlcjpCBsU,41357
+spacr/io.py,sha256=bOfKwTqo5Z4YtS2E9PB5JVOvn1NkUJKeYxg8nDdGdGE,151762
 spacr/logger.py,sha256=lJhTqt-_wfAunCPl93xE65Wr9Y1oIHJWaZMjunHUeIw,1538
-spacr/measure.py,sha256=jmOnLBudq3TuY723Cfo1EJBn67P6rlEvL6I-2FSkUgI,55315
+spacr/measure.py,sha256=Z3u4BU5RzcY82IZuboQ0OsxuXaPVwOlH65Rw6FrL5z4,55045
 spacr/mediar.py,sha256=FwLvbLQW5LQzPgvJZG8Lw7GniA2vbZx6Jv6vIKu7I5c,14743
 spacr/ml.py,sha256=MrIAtUUxMOibWVL1SjCUnYlizawCp3l3SeY4Y9yEsPw,97251
 spacr/openai.py,sha256=5vBZ3Jl2llYcW3oaTEXgdyCB2aJujMUIO5K038z7w_A,1246
-spacr/plot.py,sha256=p4AY5EWmVNPMqFD0I4NARJkvJA5gTErbDDYqDMU18pc,169479
+spacr/plot.py,sha256=Q5TbsR2NUWhA7z4HyF_2_FAEBFSNMU-G3UNDbRzW6mM,169485
 spacr/sequencing.py,sha256=ClUfwPPK6rNUbUuiEkzcwakzVyDKKUMv9ricrxT8qQY,25227
-spacr/settings.py,sha256=e6QWZ5o6Im02_t-3GQh3H4kksMTQmIZ1Rbh3BeQmmsw,84000
+spacr/settings.py,sha256=72bhOwr0U83uoWwaKtSNZucYhpgwTP1_GItRk9f6A6c,87592
 spacr/sim.py,sha256=1xKhXimNU3ukzIw-3l9cF3Znc_brW8h20yv8fSTzvss,71173
+spacr/sp_stats.py,sha256=mbhwsyIqt5upsSD346qGjdCw7CFBa0tIS7zHU9e0jNI,9536
 spacr/stats.py,sha256=mbhwsyIqt5upsSD346qGjdCw7CFBa0tIS7zHU9e0jNI,9536
-spacr/submodules.py,sha256=e_JNMGBHakEra_2pstHFmgI1NhF9TybfvTNDAegVsl0,67626
+spacr/submodules.py,sha256=jFlJeVNuIEf63TtCOpTlOZ4iiSLr238kRBiGAAAgKE4,67626
 spacr/timelapse.py,sha256=KGfG4L4-QnFfgbF7L6C5wL_3gd_rqr05Foje6RsoTBg,39603
 spacr/toxo.py,sha256=TmuhejSIPLBvsgeblsUgSvBFCR1gOkApyTKidooJ5Us,26044
-spacr/utils.py,sha256=m4MZiNbmQpZD78eu5DNmxk4cU_tk2VeVLCe_R_7YShY,226287
+spacr/utils.py,sha256=v13vzgEQwUnQAtQya_akKIkem26-0Nn5j9uhx_NcJXQ,228599
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/resources/MEDIAR/.gitignore,sha256=Ff1q9Nme14JUd-4Q3jZ65aeQ5X4uttptssVDgBVHYo8,152
 spacr/resources/MEDIAR/LICENSE,sha256=yEj_TRDLUfDpHDNM0StALXIt6mLqSgaV2hcCwa6_TcY,1065
@@ -152,9 +153,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
-spacr-0.4.0.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.4.0.dist-info/METADATA,sha256=uloYFy8DrWtHZvy5W47jBRNUEF_SeX4nLZ0OL2wMizc,6072
-spacr-0.4.0.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-spacr-0.4.0.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.4.0.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.4.0.dist-info/RECORD,,
+spacr-0.4.2.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.4.2.dist-info/METADATA,sha256=1yh08ENDvMjQGyCKwh6BX5j78vwd9JyE8JlBzpkYg7o,6095
+spacr-0.4.2.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+spacr-0.4.2.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.4.2.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.4.2.dist-info/RECORD,,