scitex 2.0.0__py2.py3-none-any.whl

scitex/general/__init__.py

@@ -0,0 +1,5 @@
+#!/usr/bin/env python3
+"""Scitex general - general utilities (currently empty)."""
+
+# This module is currently empty but preserved for compatibility
+__all__ = []

scitex/gists/_SigMacro_processFigure_S.py

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+def sigmacro_process_figure_s():
+    """Print a macro for SigmaPlot (v12.0) to format a panel.
+    
+    Please refer to the 'Automating Routine Tasks' section of the official documentation.
+    """
+    print(
+        """
+Option Explicit
+
+' Constants for FLAG_SET_BIT and FLAG_CLEAR_BIT should be defined
+Const FLAG_SET_BIT As Long = 1 ' Assuming value, replace with actual value
+Const FLAG_CLEAR_BIT As Long = 0 ' Assuming value, replace with actual value
+
+' Function to set option flag bits on
+Function FlagOn(flag As Long) As Long
+    FlagOn = flag Or FLAG_SET_BIT
+End Function
+
+' Function to set option flag bits off
+Function FlagOff(flag As Long) As Long
+    FlagOff = flag And Not FLAG_CLEAR_BIT
+End Function
+
+' Procedure to set the title size to 8 points
+Sub setTitleSize()
+    ActiveDocument.CurrentPageItem.GraphPages(0).CurrentPageObject(GPT_GRAPH).NameObject.SetObjectCurrent
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETOBJECTATTR, STA_SIZE, "111") ' Size set to 8 points
+End Sub
+
+' Procedure to set label size for a given dimension to 8 points
+Sub setLabelSize(dimension)
+    ' ActiveDocument.CurrentPageItem.GraphPages(0).CurrentPageObject(GPT_GRAPH).NameObject.SetObjectCurrent
+    ActiveDocument.CurrentPageItem.GraphPages(0).CurrentPageObject(GPT_AXIS).NameObject.SetObjectCurrent
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SLA_SELECTDIM, dimension)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETOBJECTATTR, STA_SIZE, "111") ' Size set to 8 points
+End Sub
+
+' Procedure to set tick label size for a given dimension to 7 points
+Sub setTickLabelSize(dimension)
+    ActiveDocument.CurrentPageItem.GraphPages(0).CurrentPageObject(GPT_GRAPH).NameObject.SetObjectCurrent
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SLA_SELECTDIM, dimension)
+    ActiveDocument.CurrentPageItem.GraphPages(0).CurrentPageObject(GPT_AXIS).TickLabelAttributes(SAA_LINE_MAJORTIC).SetObjectCurrent
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETOBJECTATTR, STA_SIZE, "97") ' Size set to 7 points
+End Sub
+
+' Procedure to process tick settings for a given dimension
+Sub processTicks(dimension)
+    ' Ensure the object is correctly targeted before setting attributes
+    ActiveDocument.CurrentPageItem.GraphPages(0).CurrentPageObject(GPT_AXIS).NameObject.SetObjectCurrent
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SLA_SELECTDIM, dimension)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETAXISATTR, SAA_SELECTLINE, 1)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETAXISATTR, SEA_THICKNESS, &H00000008)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETAXISATTR, SAA_TICSIZE, &H00000020)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETAXISATTR, SAA_SELECTLINE, 2)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETAXISATTR, SEA_THICKNESS, &H00000008)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETAXISATTR, SAA_TICSIZE, &H00000020)    
+End Sub
+
+' Procedure to remove an axis for a given dimension
+Sub removeAxis(dimension)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SLA_SELECTDIM, dimension)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETAXISATTR, SAA_SUB2OPTIONS, &H00000000)
+End Sub
+
+Sub resizeFigure
+	ActiveDocument.CurrentPageItem.GraphPages(0).CurrentPageObject(GPT_GRAPH).NameObject.SetObjectCurrent
+    With ActiveDocument.CurrentPageItem.GraphPages(0).CurrentPageObject(GPT_GRAPH)
+	'.Top = 0
+	'.Left = 0
+	.Width = &H000004F5&
+	.Height = &H00000378&
+	End With
+End Sub
+
+' Main procedure
+Sub Main()
+    Dim FullPATH As String
+    Dim OrigPageName As String
+    Dim ObjectType As String
+    Dim COLOR As Long
+    
+    ' Saves the original page to jump back
+    FullPATH = ActiveDocument.FullName
+    OrigPageName = ActiveDocument.CurrentPageItem.Name
+    ActiveDocument.NotebookItems(OrigPageName).IsCurrentBrowserEntry = True
+
+	' Code to set the figure size should be implemented here    
+    resizeFigure
+
+    ' Set the title sizes
+    setTitleSize
+
+    ' Set the sizes of X/Y labels
+    setLabelSize(1) ' X-axis
+    setLabelSize(2) ' Y-axis
+    
+    ' Set the sizes of X/Y tick labels
+    setTickLabelSize(1) ' X-axis
+    setTickLabelSize(2) ' Y-axis
+
+    ' Set tick length and width
+    processTicks(1) ' X-axis
+    processTicks(2) ' Y-axis
+    
+    ' Remove right and top axes
+    removeAxis(1) ' Right axis
+    removeAxis(2) ' Top axis
+    
+    ' Go back to the original page
+	Notebooks(FullPATH).NotebookItems(OrigPageName).Open
+ 
+End Sub
+    """
+    )
+
+
+# Backward compatibility alias
+import warnings
+
+
+def SigMacro_processFigure_S():
+    """Deprecated: Use sigmacro_process_figure_s() instead."""
+    warnings.warn(
+        "SigMacro_processFigure_S is deprecated, use sigmacro_process_figure_s() instead",
+        DeprecationWarning,
+        stacklevel=2
+    )
+    return sigmacro_process_figure_s()

scitex/gists/_SigMacro_toBlue.py

@@ -0,0 +1,172 @@
+def sigmacro_to_blue():
+    """Print a macro for SigmaPlot (v12.0) that changes the color and style of the selected object.
+    
+    Please refer to the 'Automating Routine Tasks' section of the official documentation.
+    """
+    print(
+        """
+Option Explicit
+
+Function FlagOn(flag As Long) As Long
+    FlagOn = flag Or FLAG_SET_BIT ' Use to set option flag bits on, leaving others unchanged
+End Function
+
+Function FlagOff(flag As Long) As Long
+    FlagOff = flag Or FLAG_CLEAR_BIT ' Use to set option flag bits off, leaving others unchanged
+End Function
+
+Function getColor(colorName As String) As Long
+    Select Case colorName
+
+        Case "Black"
+            getColor = RGB(0, 0, 0)
+        Case "Gray"
+            getColor = RGB(128, 128, 128)            
+        Case "White"
+            getColor = RGB(255, 255, 255)    
+    
+    
+        Case "Blue"
+            getColor = RGB(0, 128, 192)
+        Case "Green"
+            getColor = RGB(20, 180, 20)            
+        Case "Red"
+            getColor = RGB(255, 70, 50)
+    
+    
+        Case "Yellow"
+            getColor = RGB(230, 160, 20)
+        Case "Purple"
+            getColor = RGB(200, 50, 255)
+    
+    
+        Case "Pink"
+            getColor = RGB(255, 150, 200)            
+        Case "LightBlue"
+            getColor = RGB(20, 200, 200)
+    
+    
+        Case "DarkBlue"
+            getColor = RGB(0, 0, 100)
+        Case "Dan"
+            getColor = RGB(228, 94, 50)
+        Case "Brown"
+            getColor = RGB(128, 0, 0)            
+
+        Case Else
+            ' Default or error handling
+            getColor = RGB(0, 0, 0) ' Returning black as default or for an unrecognized color
+    End Select
+End Function
+
+
+Sub updatePlot(COLOR As Long)
+    ActiveDocument.CurrentPageItem.GraphPages(0).CurrentPageObject(GPT_GRAPH).NameObject.SetObjectCurrent
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SEA_COLOR, COLOR)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SEA_COLORREPEAT, &H00000002&)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SEA_THICKNESS, &H00000005&) ' .12 mm = .047 Inches
+End Sub
+
+Sub updateScatter(COLOR As Long)
+    ActiveDocument.CurrentPageItem.GraphPages(0).CurrentPageObject(GPT_GRAPH).NameObject.SetObjectCurrent
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SSA_EDGECOLOR, COLOR)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SSA_COLOR, COLOR)
+    ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SSA_COLORREPEAT, &H00000002&)
+	ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SSA_SIZE, &H00000020&) ' .8 mm = .032 inch
+    ' fixme scattersize=0.032 Innches
+End Sub
+Sub updateSolid(COLOR As Long)
+	ActiveDocument.CurrentPageItem.GraphPages(0).CurrentPageObject(GPT_GRAPH).NameObject.SetObjectCurrent
+	ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SDA_COLOR, COLOR)
+	ActiveDocument.CurrentPageItem.SetCurrentObjectAttribute(GPM_SETPLOTATTR, SDA_COLORREPEAT, &H00000002&)
+End Sub
+
+
+
+Function findObjectType() As String
+    On Error GoTo ErrorHandler
+
+    Dim ObjectType As Variant
+    Dim object_type As Variant 
+	object_type = ActiveDocument.CurrentPageItem.GraphPages(0).CurrentPageObject(GPT_GRAPH).Plots(0).GetAttribute(SLA_TYPE, ObjectType)	
+
+    If object_type = False Then
+        findObjectType = "Error: Failed to get object type."
+        Exit Function
+    End If
+
+    ' Map the ObjectType to a string
+    Select Case object_type
+        Case SLA_TYPE_SCATTER
+            findObjectType = "Scatter/Line"
+        Case SLA_TYPE_BAR
+            findObjectType = "Bar"
+        Case SLA_TYPE_STACKED
+            findObjectType = "Stacked Bar"
+        Case SLA_TYPE_TUKEY
+            findObjectType = "Box"
+        Case SLA_TYPE_3DSCATTER
+            findObjectType = "3D Scatter/Line"
+        Case Else
+            findObjectType = "Unknown Object Type: " & object_type
+    End Select
+    Exit Function
+
+ErrorHandler:
+    findObjectType = "An error has occurred: " & Err.Description
+End Function
+
+Sub Main()
+    On Error GoTo ErrorHandler
+
+	Dim FullPATH As String
+    Dim OrigPageName As String
+    Dim ObjectType As String
+    Dim COLOR As Long
+    
+    ' Remember the original page
+    FullPATH = ActiveDocument.FullName
+    OrigPageName = ActiveDocument.CurrentPageItem.Name
+    ActiveDocument.NotebookItems(OrigPageName).IsCurrentBrowserEntry = True
+
+    ' Get the color value for blue
+    COLOR = getColor("Blue")
+    
+    ' Find the type of the object
+    ObjectType = findObjectType()
+    
+    ' Check the object type and call the corresponding update function
+    If ObjectType = "Scatter/Line" Or ObjectType = "3D Scatter/Line" Then
+        updatePlot COLOR
+        updateScatter COLOR
+    ElseIf ObjectType = "Bar" Or ObjectType = "Stacked Bar" Or ObjectType = "Box" Then
+        updateSolid COLOR
+    Else
+        ' Raise a custom error
+        Err.Raise vbObjectError + 513, "Main", "Unknown or unsupported object type: " & ObjectType
+    End If
+    
+    ' Go back to the original page
+	Notebooks(FullPATH).NotebookItems(OrigPageName).Open
+	
+    Exit Sub
+
+ErrorHandler:
+    MsgBox "An error has occurred: " & Err.Description
+End Sub
+"""
+    )
+
+
+# Backward compatibility alias
+import warnings
+
+
+def SigMacro_toBlue():
+    """Deprecated: Use sigmacro_to_blue() instead."""
+    warnings.warn(
+        "SigMacro_toBlue is deprecated, use sigmacro_to_blue() instead",
+        DeprecationWarning,
+        stacklevel=2
+    )
+    return sigmacro_to_blue()

scitex/gists/__init__.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python3
+"""Scitex gists module."""
+
+from ._SigMacro_processFigure_S import SigMacro_processFigure_S, sigmacro_process_figure_s
+from ._SigMacro_toBlue import SigMacro_toBlue, sigmacro_to_blue
+
+__all__ = [
+    "SigMacro_processFigure_S",
+    "SigMacro_toBlue",
+    "sigmacro_process_figure_s",
+    "sigmacro_to_blue",
+]

scitex/io/_H5Explorer.py

@@ -0,0 +1,292 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-06-14 18:05:18 (ywatanabe)"
+# File: /ssh:sp:/home/ywatanabe/proj/SciTeX-Code/src/scitex/io/_H5Explorer.py
+# ----------------------------------------
+import os
+__FILE__ = (
+    "./src/scitex/io/_H5Explorer.py"
+)
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
+import warnings
+
+# Time-stamp: "2025-06-13 21:00:00 (ywatanabe)"
+
+"""HDF5 file explorer for interactive data inspection."""
+
+from typing import Any, Dict, List, Optional
+
+import h5py
+import numpy as np
+
+
+class H5Explorer:
+    """Interactive HDF5 file explorer.
+
+    This class provides convenient methods to explore HDF5 files,
+    inspect their structure, and load data.
+
+    Example:
+        >>> explorer = H5Explorer('data.h5')
+        >>> explorer.explore()  # Display file structure
+        >>> data = explorer.load('group1/dataset1')  # Load specific dataset
+        >>> explorer.close()
+    """
+
+    def __init__(self, filepath: str, mode: str = "r"):
+        """Initialize H5Explorer.
+
+        Args:
+            filepath: Path to HDF5 file
+            mode: File opening mode ('r' for read, 'r+' for read/write)
+        """
+        self.filepath = filepath
+        self.mode = mode
+        self.file = h5py.File(filepath, mode)
+
+    def __enter__(self):
+        """Context manager entry."""
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        """Context manager exit."""
+        self.close()
+
+    def close(self):
+        """Close the HDF5 file."""
+        if hasattr(self, "file") and self.file:
+            self.file.close()
+
+    def explore(
+        self, path: str = "/", max_depth: Optional[int] = None
+    ) -> None:
+        """Explore HDF5 file structure interactively."""
+        self.show(path, max_depth)
+
+    def show(
+        self,
+        path: str = "/",
+        max_depth: Optional[int] = None,
+        indent: str = "",
+        _current_depth: int = 0,
+    ) -> None:
+        """Display HDF5 file structure.
+
+        Args:
+            path: Starting path in HDF5 file
+            max_depth: Maximum depth to explore (None for unlimited)
+            indent: Indentation string (used internally)
+            _current_depth: Current depth (used internally)
+        """
+        if max_depth is not None and _current_depth > max_depth:
+            return
+
+        item = self.file[path] if path != "/" else self.file
+
+        if isinstance(item, h5py.Group):
+            if path != "/":
+                print(f"{indent}[{path.split('/')[-1]}]")
+            for key in sorted(item.keys()):
+                subpath = f"{path}/{key}".replace("//", "/")
+                self.show(
+                    subpath, max_depth, indent + "  ", _current_depth + 1
+                )
+        elif isinstance(item, h5py.Dataset):
+            name = path.split("/")[-1]
+            shape = item.shape
+            dtype = item.dtype
+            size = item.size
+            print(f"{indent}{name}: shape={shape}, dtype={dtype}, size={size}")
+
+    def keys(self, path: str = "/") -> List[str]:
+        """Get keys at specified path.
+
+        Args:
+            path: Path in HDF5 file
+
+        Returns:
+            List of keys at the specified path
+        """
+        item = self.file[path] if path != "/" else self.file
+        if isinstance(item, h5py.Group):
+            return list(item.keys())
+        return []
+
+    def load(self, path: str) -> Any:
+        """Load data from specified path.
+
+        Args:
+            path: Path to dataset or group in HDF5 file
+
+        Returns:
+            Data from the specified path
+        """
+        item = self.file[path]
+
+        if isinstance(item, h5py.Dataset):
+            data = item[()]
+            # Decode bytes to string if needed
+            if isinstance(data, bytes):
+                return data.decode("utf-8")
+            # Handle pickled objects (stored as np.void)
+            elif isinstance(data, np.void):
+                import pickle
+                return pickle.loads(data.tobytes())
+            return data
+        elif isinstance(item, h5py.Group):
+            # Load group as dictionary
+            result = {}
+            for key in item.keys():
+                result[key] = self.load(f"{path}/{key}".replace("//", "/"))
+            # Also load attributes
+            for key in item.attrs.keys():
+                result[f"_attr_{key}"] = item.attrs[key]
+            return result
+        else:
+            return item
+
+    def get(self, path: str) -> Any:
+        """Alias for load() method for compatibility.
+
+        Args:
+            path: Path to dataset or group in HDF5 file
+
+        Returns:
+            Data from the specified path
+        """
+        return self.load(path)
+
+    def get_info(self, path: str = "/") -> Dict[str, Any]:
+        """Get information about an item.
+
+        Args:
+            path: Path to item in HDF5 file
+
+        Returns:
+            Dictionary with item information
+        """
+        item = self.file[path] if path != "/" else self.file
+
+        info = {
+            "path": path,
+            "type": type(item).__name__,
+        }
+
+        if isinstance(item, h5py.Dataset):
+            info.update(
+                {
+                    "shape": item.shape,
+                    "dtype": str(item.dtype),
+                    "size": item.size,
+                    "compression": item.compression,
+                    "chunks": item.chunks,
+                }
+            )
+        elif isinstance(item, h5py.Group):
+            info["n_items"] = len(item.keys())
+            info["keys"] = list(item.keys())
+
+        # Add attributes
+        if hasattr(item, "attrs") and len(item.attrs) > 0:
+            info["attributes"] = dict(item.attrs)
+
+        return info
+
+    def find(self, pattern: str, path: str = "/") -> List[str]:
+        """Find items matching pattern.
+
+        Args:
+            pattern: Pattern to search for in item names
+            path: Starting path for search
+
+        Returns:
+            List of paths matching the pattern
+        """
+        matches = []
+
+        def _search(current_path):
+            item = (
+                self.file[current_path] if current_path != "/" else self.file
+            )
+
+            if isinstance(item, h5py.Group):
+                for key in item.keys():
+                    subpath = f"{current_path}/{key}".replace("//", "/")
+                    if pattern.lower() in key.lower():
+                        matches.append(subpath)
+                    _search(subpath)
+            elif pattern.lower() in current_path.split("/")[-1].lower():
+                matches.append(current_path)
+
+        _search(path)
+        return matches
+
+    def get_shape(self, path: str) -> Optional[tuple]:
+        """Get shape of a dataset.
+
+        Args:
+            path: Path to dataset
+
+        Returns:
+            Shape tuple or None if not a dataset
+        """
+        item = self.file[path]
+        if isinstance(item, h5py.Dataset):
+            return item.shape
+        return None
+
+    def get_dtype(self, path: str) -> Optional[np.dtype]:
+        """Get dtype of a dataset.
+
+        Args:
+            path: Path to dataset
+
+        Returns:
+            Numpy dtype or None if not a dataset
+        """
+        item = self.file[path]
+        if isinstance(item, h5py.Dataset):
+            return item.dtype
+        return None
+
+
+# Convenience function
+
+
+def explore_h5(filepath: str) -> None:
+    """Explore HDF5 file structure.
+
+    Args:
+        filepath: Path to HDF5 file
+    """
+    if os.path.exists(filepath):
+        explorer = H5Explorer(filepath)
+        explorer.explore()
+        explorer.close()
+    else:
+        warnings.warn(f"Warning: File does not exist: {filepath}")
+
+
+def has_h5_key(h5_path, key):
+    """Check if key exists in HDF5 file."""
+    h5_path = os.path.realpath(h5_path)
+
+    if not os.path.exists(h5_path):
+        return False
+
+    try:
+        with h5py.File(h5_path, "r") as h5_file:
+            parts = key.split("/")
+            current = h5_file
+            for part in parts:
+                if part in current:
+                    current = current[part]
+                else:
+                    return False
+            return True
+
+    except (KeyError, FileNotFoundError, OSError):
+        return False
+
+# EOF

scitex/io/__init__.py

@@ -0,0 +1,82 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-06-14 16:00:50 (ywatanabe)"
+# File: /ssh:sp:/home/ywatanabe/proj/SciTeX-Code/src/scitex/io/__init__.py
+# ----------------------------------------
+import os
+__FILE__ = (
+    "./src/scitex/io/__init__.py"
+)
+__DIR__ = os.path.dirname(__FILE__)
+# ----------------------------------------
+"""Scitex IO module with lazy imports to avoid circular dependencies."""
+
+# Import commonly used functions directly
+from ._save import save
+from ._load import load
+from ._load_configs import load_configs
+from ._glob import glob, parse_glob
+from ._reload import reload
+from ._flush import flush
+from ._cache import cache
+from ._H5Explorer import H5Explorer, explore_h5, has_h5_key
+
+# Import save module functions
+try:
+    from ._save_modules import (
+        save_image,
+        save_text,
+        save_mp4,
+        save_listed_dfs_as_csv,
+        save_listed_scalars_as_csv,
+        save_optuna_study_as_csv_and_pngs,
+    )
+except ImportError as e:
+    # Fallback for missing functions
+    save_image = None
+    save_text = None
+    save_mp4 = None
+    save_listed_dfs_as_csv = None
+    save_listed_scalars_as_csv = None
+    save_optuna_study_as_csv_and_pngs = None
+
+# Optional imports that might fail
+try:
+    from ._path import path
+except ImportError:
+    path = None
+
+try:
+    from ._mv_to_tmp import mv_to_tmp
+except ImportError:
+    mv_to_tmp = None
+
+try:
+    from ._json2md import json2md
+except ImportError:
+    json2md = None
+
+__all__ = [
+    "save",
+    "load",
+    "load_configs",
+    "glob",
+    "parse_glob",
+    "reload",
+    "flush",
+    "cache",
+    "H5Explorer",
+    "explore_h5",
+    "has_h5_key",
+    "path",
+    "mv_to_tmp",
+    "json2md",
+    "save_image",
+    "save_text",
+    "save_mp4",
+    "save_listed_dfs_as_csv",
+    "save_listed_scalars_as_csv",
+    "save_optuna_study_as_csv_and_pngs",
+]
+
+# EOF