scitex 2.5.0__py3-none-any.whl → 2.7.0__py3-none-any.whl

scitex/nn/__init__.py

@@ -3,11 +3,24 @@
 
 from ._AxiswiseDropout import AxiswiseDropout
 from ._BNet import BHead as BHead_v1, BNet as BNet_v1, BNet_config as BNet_config_v1
-from ._BNet_Res import BHead as BHead_Res, BNet as BNet_Res, BNet_config as BNet_config_Res
+from ._BNet_Res import (
+    BHead as BHead_Res,
+    BNet as BNet_Res,
+    BNet_config as BNet_config_Res,
+)
 from ._ChannelGainChanger import ChannelGainChanger
 from ._DropoutChannels import DropoutChannels
-from ._Filters import BandPassFilter, BandStopFilter, BaseFilter1D, DifferentiableBandPassFilter, GaussianFilter, HighPassFilter, LowPassFilter
+from ._Filters import (
+    BandPassFilter,
+    BandStopFilter,
+    BaseFilter1D,
+    DifferentiableBandPassFilter,
+    GaussianFilter,
+    HighPassFilter,
+    LowPassFilter,
+)
 from ._FreqGainChanger import FreqGainChanger
+
 # Removed duplicate GaussianFilter import - already imported from _Filters
 from ._Hilbert import Hilbert
 from ._MNet_1000 import MNet1000, MNet_1000, MNet_config, ReshapeLayer, SwapLayer
@@ -24,7 +37,7 @@ from ._Wavelet import Wavelet
 __all__ = [
     "AxiswiseDropout",
     "BHead_v1",
-    "BHead_Res", 
+    "BHead_Res",
     "BNet_v1",
     "BNet_Res",
     "BNet_config_v1",

scitex/path/_clean.py

@@ -5,6 +5,7 @@
 
 import os
 
+
 def clean(path_string):
     """Cleans and normalizes a file system path string.
 
@@ -28,29 +29,30 @@ def clean(path_string):
         Normalized path string
     """
     # Convert Path objects to strings to avoid AttributeError
-    if hasattr(path_string, '__fspath__'):  # Check if it's a path-like object
+    if hasattr(path_string, "__fspath__"):  # Check if it's a path-like object
         path_string = str(path_string)
-        
+
     if not path_string:
         return ""
-    
+
     # Remember if path ends with a slash (indicating a directory)
     is_directory = path_string.endswith("/")
-    
+
     # Replace spaces with underscores
     path_string = path_string.replace(" ", "_")
-    
+
     # Use normpath to handle ../ and ./ references
     cleaned_path = os.path.normpath(path_string)
-    
+
     # Replace multiple slashes with single slash
     while "//" in cleaned_path:
         cleaned_path = cleaned_path.replace("//", "/")
-        
+
     # Restore trailing slash if it was a directory
     if is_directory and not cleaned_path.endswith("/"):
         cleaned_path += "/"
-        
+
     return cleaned_path
 
+
 # EOF

scitex/path/_find.py

@@ -94,7 +94,7 @@ if __name__ == "__main__":
         import matplotlib.pyplot as plt
     except ImportError:
         plt = None
-    
+
     # Start
     CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(sys, plt)
 

scitex/path/_get_spath.py

@@ -10,7 +10,6 @@ from ._split import split
 
 
 def get_spath(sfname=".", makedirs=False):
-
     # if __IPYTHON__:
     #     THIS_FILE = f'/tmp/{os.getenv("USER")}.py'
     # else:
@@ -18,7 +17,7 @@ def get_spath(sfname=".", makedirs=False):
 
     THIS_FILE = inspect.stack()[1].filename
     if "ipython" in __file__:  # for ipython
-        THIS_FILE = f'/tmp/{os.getenv("USER")}.py'
+        THIS_FILE = f"/tmp/{os.getenv('USER')}.py"
 
     ## spath
     fpath = __file__

scitex/path/_mk_spath.py

@@ -34,7 +34,7 @@ def mk_spath(sfname, makedirs=False):
     """
     THIS_FILE = inspect.stack()[1].filename
     if "ipython" in __file__:  # for ipython
-        THIS_FILE = f'/tmp/fake-{os.getenv("USER")}.py'
+        THIS_FILE = f"/tmp/fake-{os.getenv('USER')}.py"
 
     ## spath
     fpath = __file__

scitex/path/_symlink.py

@@ -5,6 +5,7 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -117,9 +118,7 @@ def symlink(
         else:
             src_for_link = src_path.absolute()
 
-        dst_path.symlink_to(
-            src_for_link, target_is_directory=target_is_directory
-        )
+        dst_path.symlink_to(src_for_link, target_is_directory=target_is_directory)
         logger.success(f"Created symlink: {dst_path} -> {src_for_link}")
 
     except OSError as e:
@@ -249,9 +248,7 @@ def unlink_symlink(path: Union[str, Path], missing_ok: bool = True) -> None:
     # logger.info(f"Removed symlink: {path}")
 
 
-def list_symlinks(
-    directory: Union[str, Path], recursive: bool = False
-) -> list[Path]:
+def list_symlinks(directory: Union[str, Path], recursive: bool = False) -> list[Path]:
     """
     List all symbolic links in a directory.
 
@@ -319,10 +316,7 @@ def fix_broken_symlinks(
         try:
             # Check if target exists
             target = Path(os.readlink(link))
-            if (
-                not link.parent.joinpath(target).exists()
-                and not target.is_absolute()
-            ):
+            if not link.parent.joinpath(target).exists() and not target.is_absolute():
                 # Relative link with non-existent target
                 result["found"].append(link)
             elif target.is_absolute() and not target.exists():
@@ -345,4 +339,5 @@ def fix_broken_symlinks(
 
     return result
 
+
 # EOF

scitex/pd/__init__.py

@@ -6,7 +6,10 @@ from ._find_pval import find_pval, _find_pval_col
 from ._force_df import force_df
 from ._from_xyz import from_xyz
 from ._get_unique import get_unique
-from ._ignore_SettingWithCopyWarning import ignore_SettingWithCopyWarning, ignore_setting_with_copy_warning
+from ._ignore_SettingWithCopyWarning import (
+    ignore_SettingWithCopyWarning,
+    ignore_setting_with_copy_warning,
+)
 from ._melt_cols import melt_cols
 from ._merge_columns import merge_cols, merge_columns
 from ._mv import mv, mv_to_first, mv_to_last

scitex/pd/_force_df.py

@@ -18,31 +18,31 @@ from scitex.types import is_listed_X
 def force_df(data, filler=np.nan):
     """
     Convert various data types to pandas DataFrame.
-    
+
     Parameters
     ----------
     data : various
-        The data to convert to DataFrame. Can be DataFrame, Series, ndarray, 
+        The data to convert to DataFrame. Can be DataFrame, Series, ndarray,
         list, tuple, dict, scalar value, etc.
     filler : any, optional
         Value to use for filling missing values, by default np.nan
-        
+
     Returns
     -------
     pd.DataFrame
         Data converted to DataFrame
-        
+
     Examples
     --------
     >>> import scitex
     >>> import pandas as pd
     >>> import numpy as np
-    
+
     # DataFrame input returns the same DataFrame
     >>> df = pd.DataFrame({'A': [1, 2, 3], 'B': [4, 5, 6]})
     >>> scitex.pd.force_df(df) is df
     True
-    
+
     # Series input is converted to DataFrame
     >>> series = pd.Series([1, 2, 3], name='test')
     >>> scitex.pd.force_df(series)
@@ -50,7 +50,7 @@ def force_df(data, filler=np.nan):
     0     1
     1     2
     2     3
-    
+
     # NumPy array input is converted to DataFrame
     >>> arr = np.array([1, 2, 3])
     >>> scitex.pd.force_df(arr)
@@ -58,19 +58,19 @@ def force_df(data, filler=np.nan):
     0      1
     1      2
     2      3
-    
+
     # Scalar values are converted to single-value DataFrames
     >>> scitex.pd.force_df(42)
        value
     0     42
-    
+
     # Lists and tuples are converted to DataFrame
     >>> scitex.pd.force_df([1, 2, 3])
        value
     0      1
     1      2
     2      3
-    
+
     # Dictionaries are converted to DataFrame with appropriate handling
     # of different length values
     >>> data = {'A': [1, 2, 3], 'B': [4, 5]}
@@ -83,20 +83,20 @@ def force_df(data, filler=np.nan):
     # Return None as empty DataFrame
     if data is None:
         return pd.DataFrame()
-        
+
     # Return DataFrame as is
     if isinstance(data, pd.DataFrame):
         return data
-        
+
     # Convert Series to DataFrame
     if isinstance(data, pd.Series):
         return data.to_frame()
-        
+
     # Convert numpy array to DataFrame
     if isinstance(data, np.ndarray):
         # Handle 1D array
         if data.ndim == 1:
-            return pd.DataFrame(data, columns=['value'])
+            return pd.DataFrame(data, columns=["value"])
         # Handle 2D array
         elif data.ndim == 2:
             return pd.DataFrame(data)
@@ -105,11 +105,11 @@ def force_df(data, filler=np.nan):
             shape = data.shape
             reshaped = data.reshape(shape[0], -1)
             return pd.DataFrame(reshaped)
-            
+
     # Handle scalar values (int, float, str, etc.)
     if isinstance(data, (int, float, str, bool)):
-        return pd.DataFrame([data], columns=['value'])
-            
+        return pd.DataFrame([data], columns=["value"])
+
     # Handle lists and tuples
     if isinstance(data, (list, tuple)):
         # Handle list of lists/arrays -> DataFrame
@@ -117,13 +117,13 @@ def force_df(data, filler=np.nan):
             return pd.DataFrame(data)
         # Handle simple list/tuple -> single column DataFrame
         else:
-            return pd.DataFrame(data, columns=['value'])
-    
+            return pd.DataFrame(data, columns=["value"])
+
     # Continue with the original implementation for dictionaries
     if isinstance(data, dict):
         # Original implementation
         permutable_dict = data.copy()
-        
+
         # Get the lengths
         max_len = 0
         for k, v in permutable_dict.items():
@@ -133,20 +133,20 @@ def force_df(data, filler=np.nan):
             else:
                 length = len(v)
             max_len = max(max_len, length)
-        
+
         # Replace with appropriately filled list
         for k, v in permutable_dict.items():
             if isinstance(v, (str, int, float)) or not hasattr(v, "__len__"):
                 permutable_dict[k] = [v] + [filler] * (max_len - 1)
             else:
                 permutable_dict[k] = list(v) + [filler] * (max_len - len(v))
-        
+
         # Puts them into a DataFrame
         return pd.DataFrame(permutable_dict)
-    
+
     # For any other iterable type
     try:
-        return pd.DataFrame(list(data), columns=['value'])
+        return pd.DataFrame(list(data), columns=["value"])
     except:
         raise TypeError(f"Cannot convert object of type {type(data)} to DataFrame")
 

scitex/pd/_get_unique.py

@@ -5,6 +5,7 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------

scitex/pd/_merge_columns.py

@@ -18,7 +18,7 @@ def merge_columns(
     sep: str = None,
     sep1: str = "_",
     sep2: str = "-",
-    name: str = "merged"
+    name: str = "merged",
 ) -> pd.DataFrame:
     """Creates a new column by joining specified columns.
 

scitex/pd/_round.py

@@ -41,27 +41,31 @@ def round(df: pd.DataFrame, factor: int = 3) -> pd.DataFrame:
         if pd.api.types.is_string_dtype(column):
             return column
         # Note: boolean types are allowed to be converted to numeric
-        if pd.api.types.is_object_dtype(column) and not pd.api.types.is_numeric_dtype(column) and not pd.api.types.is_bool_dtype(column):
+        if (
+            pd.api.types.is_object_dtype(column)
+            and not pd.api.types.is_numeric_dtype(column)
+            and not pd.api.types.is_bool_dtype(column)
+        ):
             return column
-            
+
         try:
             # Handle boolean columns explicitly
             if pd.api.types.is_bool_dtype(column):
                 return column.astype(int)
-                
+
             numeric_column = pd.to_numeric(column, errors="coerce")
             if np.issubdtype(numeric_column.dtype, np.integer):
                 return numeric_column.astype(int)
-            
+
             # For float columns, round first
             rounded = numeric_column.round(factor)
-            
+
             # If factor is 0 and all values are whole numbers, convert to int
             if factor == 0 and (rounded % 1 == 0).all() and not rounded.isna().any():
                 return rounded.astype(int)
-                
+
             return rounded
-            
+
         except (ValueError, TypeError):
             return column
 

scitex/pd/_to_xy.py

@@ -33,7 +33,6 @@ def to_xy(data_frame):
     assert data_frame.shape[0] == data_frame.shape[1]
 
     if not data_frame.index.equals(data_frame.columns):
-
         if (data_frame.index == np.array(range(len(data_frame.index)))).all():
             data_frame.columns = data_frame.index
         elif (data_frame.columns == np.array(range(len(data_frame.columns)))).all():

scitex/plt/REQUESTS.md

@@ -0,0 +1,191 @@
+# Requests for scitex.plt JSON Schema (scitex.plt.figure.recipe v0.2.0)
+
+These are requests from scitex.vis to ensure the JSON schema is compatible with
+the interactive editor and renderer.
+
+## 1. Consistent data_ref Column Naming
+
+**Issue**: The `data_ref` keys in `calls` don't match the actual CSV column names.
+
+**Current**:
+```json
+"calls": [{
+    "data_ref": {
+        "x": "ax-row-0-col-0_trace-id-ax_00_ch1_variable-x",
+        "y": "ax-row-0-col-0_trace-id-ax_00_ch1_variable-y"
+    }
+}]
+```
+
+**CSV columns** (from `columns_actual`):
+```
+"ax-row-0-col-0_trace-id-ch1_variable-x"
+"ax-row-0-col-0_trace-id-ch1_variable-y"
+```
+
+**Note**: The `data_ref` includes `ax_00_` prefix in trace-id but CSV doesn't.
+
+**Request**: Ensure `data_ref` values exactly match CSV column names, OR document
+the mapping convention clearly.
+
+---
+
+## 2. Add Panel Titles to Axis Spec
+
+**Current**: No title field in axis spec.
+
+**Request**: Add optional `title` field to each axis:
+```json
+"ax_00": {
+    "title": "A) Multi-channel Recording",
+    "grid_position": {...},
+    "xaxis": {...},
+    ...
+}
+```
+
+---
+
+## 3. Explicit Legend Configuration Per Axis
+
+**Request**: Add legend configuration to each axis:
+```json
+"ax_00": {
+    "legend": {
+        "visible": true,
+        "loc": "upper right",
+        "frameon": false,
+        "fontsize": 6
+    }
+}
+```
+
+---
+
+## 4. Add `method_type` Classification
+
+**Request**: Add a high-level classification for rendering strategies:
+```json
+"calls": [{
+    "id": "ch1",
+    "method": "plot",
+    "method_type": "line",  // "line", "scatter", "bar", "fill", "image", "annotation"
+    ...
+}]
+```
+
+This helps the editor group similar elements and apply consistent styling.
+
+---
+
+## 5. Color Information in Calls
+
+**Current**: Colors are in `kwargs` but not always present.
+
+**Request**: Ensure color is always included for colored elements:
+```json
+"calls": [{
+    "id": "ch1",
+    "method": "plot",
+    "kwargs": {
+        "color": "#1f77b4",
+        "label": "Ch1",
+        "linewidth": 0.57
+    }
+}]
+```
+
+---
+
+## 6. Trace Grouping for Related Elements
+
+**Request**: Add optional `group` field to link related traces:
+```json
+"calls": [
+    {"id": "mean-line", "group": "mean-std", "method": "plot", ...},
+    {"id": "upper-bound", "group": "mean-std", "method": "fill_between", ...},
+    {"id": "lower-bound", "group": "mean-std", "method": "fill_between", ...}
+]
+```
+
+This allows the editor to select/edit related elements together.
+
+---
+
+## 7. Marker Information for Scatter/Point Plots
+
+**Request**: Include marker style info explicitly:
+```json
+"kwargs": {
+    "marker": "o",
+    "markersize": 6,
+    "markerfacecolor": "#1f77b4",
+    "markeredgecolor": "none"
+}
+```
+
+---
+
+## 8. Add `editable` Flag
+
+**Request**: Mark which properties are user-editable vs computed:
+```json
+"calls": [{
+    "id": "regression-line",
+    "editable": {
+        "color": true,
+        "linewidth": true,
+        "data": false  // computed from scatter data
+    }
+}]
+```
+
+---
+
+## 9. Colorbar Configuration for Heatmaps
+
+**Request**: Add colorbar spec when imshow/heatmap is used:
+```json
+"ax_02": {
+    "colorbar": {
+        "visible": true,
+        "label": "Intensity [a.u.]",
+        "orientation": "vertical"
+    }
+}
+```
+
+---
+
+## 10. Secondary Y-axis Support
+
+**Request**: Support twin axes (twinx/twiny):
+```json
+"ax_00": {
+    "grid_position": {"row": 0, "col": 0},
+    "xaxis": {...},
+    "yaxis": {...},
+    "secondary_yaxis": {
+        "label": "Mean Activity",
+        "lim": [0, 20],
+        "calls": [...]
+    }
+}
+```
+
+---
+
+## Priority
+
+| Request | Priority | Reason |
+|---------|----------|--------|
+| 1 (Column naming) | HIGH | Breaks data loading |
+| 5 (Colors in kwargs) | HIGH | Required for rendering |
+| 2 (Panel titles) | MEDIUM | UI feature |
+| 3 (Legend config) | MEDIUM | UI feature |
+| 4 (method_type) | LOW | Optimization |
+| 6-10 | LOW | Future features |
+
+---
+
+*Generated: 2025-12-10 by scitex.vis editor refactoring*