scitex 2.1.3__py3-none-any.whl → 2.4.0__py3-none-any.whl

scitex/io/utils/h5_to_zarr.py

@@ -35,7 +35,7 @@ from typing import Optional, Union, Dict, Any, List, Tuple
 import warnings
 from tqdm import tqdm
 
-from ...errors import (
+from scitex.errors import (
     IOError as SciTeXIOError,
     FileFormatError,
     PathNotFoundError,

scitex/linalg/_distance.py

@@ -6,8 +6,8 @@
 import numpy as np
 import scipy.spatial.distance as _distance
 
-from ..decorators._numpy_fn import numpy_fn
-from ..decorators._wrap import wrap
+from scitex.decorators._numpy_fn import numpy_fn
+from scitex.decorators._wrap import wrap
 
 
 @numpy_fn

scitex/linalg/_geometric_median.py

@@ -10,7 +10,7 @@ This script does XYZ.
 
 import torch
 from geom_median.torch import compute_geometric_median
-from ..decorators import torch_fn
+from scitex.decorators import torch_fn
 
 # @torch_fn
 # def geometric_median(xx, dim=-1):

scitex/logging/README.md

@@ -231,7 +231,7 @@ logger.success("Extra emphasis", c="light_green")  # Light green
 
 **Available Colors**:
 - Basic: `black`, `red`, `green`, `yellow`, `blue`, `magenta`, `cyan`, `white`, `grey`
-- Light variants: `light_red`, `light_green`, `light_yellow`, `light_blue`, `light_magenta`, `light_cyan`
+- Light variants: `light_red`, `light_green`, `light_yellow`, `lightblue`, `light_magenta`, `light_cyan`
 
 **Use Cases**:
 - Highlight critical information in INFO logs: `logger.info("msg", c="red")`

scitex/logging/_Tee.py

@@ -35,8 +35,8 @@ import re
 import sys
 from typing import Any, TextIO
 
-from ..str._clean_path import clean_path
-from ..str._printc import printc
+from scitex.str._clean_path import clean_path
+from scitex.str._printc import printc
 
 """Functions & Classes"""
 def _get_logger():

scitex/logging/_formatters.py

@@ -60,7 +60,7 @@ class SciTeXConsoleFormatter(logging.Formatter):
         "light_red": "\033[91m",
         "light_green": "\033[92m",
         "light_yellow": "\033[93m",
-        "light_blue": "\033[94m",
+        "lightblue": "\033[94m",
         "light_magenta": "\033[95m",
         "light_cyan": "\033[96m",
     }
@@ -90,7 +90,14 @@ class SciTeXConsoleFormatter(logging.Formatter):
         # Use parent formatter to apply template
         formatted = super().format(record)
 
-        if hasattr(sys.stdout, "isatty") and sys.stdout.isatty():
+        # Check if we can use colors (stdout is a tty and not closed)
+        try:
+            use_colors = hasattr(sys.stdout, "isatty") and sys.stdout.isatty()
+        except ValueError:
+            # stdout/stderr is closed
+            use_colors = False
+
+        if use_colors:
             # Check for custom color override
             custom_color = getattr(record, "color", None)
 

scitex/logging/_logger.py

@@ -16,6 +16,7 @@ __FILE__ = __file__
 """Enhanced logger class for SciTeX."""
 
 import logging
+import pprint as _pprint
 
 from ._levels import FAIL, SUCCESS
 
@@ -31,10 +32,46 @@ class SciTeXLogger(logging.Logger):
         sep=None,
         n_sep=40,
         c=None,
+        pprint=False,
         *args,
         **kwargs,
     ):
-        """Internal method to log with indent, separator, and color support."""
+        """Internal method to log with indent, separator, color, and pprint support.
+
+        Args:
+            level: Logging level
+            message: Message to log
+            indent: Number of spaces to indent
+            sep: Separator character (e.g., '=', '-')
+            n_sep: Number of separator characters
+            c: Color code
+            pprint: If True, format message using pprint for better readability
+            *args: Additional arguments
+            **kwargs: Additional keyword arguments
+        """
+        # Apply pprint formatting if requested
+        if pprint:
+            # If message is a string, keep it as is
+            # Otherwise, format it with pprint
+            if not isinstance(message, str):
+                # Convert DotDict to regular dict for better pprint support
+                # Exclude private keys (starting with _) by default
+                if hasattr(message, 'to_dict'):
+                    message = message.to_dict(include_private=False)
+                message = _pprint.pformat(message, indent=2, width=80, compact=False)
+
+            # For multi-line messages, indent all lines after the first
+            # to align with the log level prefix (e.g., "INFO: ") plus any indent
+            if '\n' in message:
+                lines = message.split('\n')
+                # Calculate the indent needed:
+                # - 6 chars for "INFO: " or "ERRO: " prefix
+                # - Plus the indent parameter for additional spacing
+                total_indent = 6 + indent
+                prefix_indent = ' ' * total_indent
+                # Join lines with proper indentation
+                message = lines[0] + '\n' + '\n'.join(prefix_indent + line for line in lines[1:])
+
         # Add separator lines if requested
         if sep is not None:
             separator = sep * n_sep
@@ -51,27 +88,27 @@ class SciTeXLogger(logging.Logger):
         self._log(level, message, args, **kwargs)
 
     def debug(
-        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, pprint=False, **kwargs
     ):
-        """Log a debug message with optional indent, separator, and color."""
+        """Log a debug message with optional indent, separator, color, and pprint."""
         if self.isEnabledFor(logging.DEBUG):
             self._log_with_indent(
-                logging.DEBUG, message, indent, sep, n_sep, c, *args, **kwargs
+                logging.DEBUG, message, indent, sep, n_sep, c, pprint, *args, **kwargs
             )
 
     def info(
-        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, pprint=False, **kwargs
     ):
-        """Log an info message with optional indent, separator, and color."""
+        """Log an info message with optional indent, separator, color, and pprint."""
         if self.isEnabledFor(logging.INFO):
             self._log_with_indent(
-                logging.INFO, message, indent, sep, n_sep, c, *args, **kwargs
+                logging.INFO, message, indent, sep, n_sep, c, pprint, *args, **kwargs
             )
 
     def warning(
-        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, pprint=False, **kwargs
     ):
-        """Log a warning message with optional indent, separator, and color."""
+        """Log a warning message with optional indent, separator, color, and pprint."""
         if self.isEnabledFor(logging.WARNING):
             self._log_with_indent(
                 logging.WARNING,
@@ -80,23 +117,24 @@ class SciTeXLogger(logging.Logger):
                 sep,
                 n_sep,
                 c,
+                pprint,
                 *args,
                 **kwargs,
             )
 
     def error(
-        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, pprint=False, **kwargs
     ):
-        """Log an error message with optional indent, separator, and color."""
+        """Log an error message with optional indent, separator, color, and pprint."""
         if self.isEnabledFor(logging.ERROR):
             self._log_with_indent(
-                logging.ERROR, message, indent, sep, n_sep, c, *args, **kwargs
+                logging.ERROR, message, indent, sep, n_sep, c, pprint, *args, **kwargs
             )
 
     def critical(
-        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, pprint=False, **kwargs
     ):
-        """Log a critical message with optional indent, separator, and color."""
+        """Log a critical message with optional indent, separator, color, and pprint."""
         if self.isEnabledFor(logging.CRITICAL):
             self._log_with_indent(
                 logging.CRITICAL,
@@ -105,26 +143,27 @@ class SciTeXLogger(logging.Logger):
                 sep,
                 n_sep,
                 c,
+                pprint,
                 *args,
                 **kwargs,
             )
 
     def success(
-        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, pprint=False, **kwargs
     ):
-        """Log a success message with optional indent, separator, and color."""
+        """Log a success message with optional indent, separator, color, and pprint."""
         if self.isEnabledFor(SUCCESS):
             self._log_with_indent(
-                SUCCESS, message, indent, sep, n_sep, c, *args, **kwargs
+                SUCCESS, message, indent, sep, n_sep, c, pprint, *args, **kwargs
             )
 
     def fail(
-        self, message, *args, indent=0, sep=None, n_sep=40, c=None, **kwargs
+        self, message, *args, indent=0, sep=None, n_sep=40, c=None, pprint=False, **kwargs
     ):
-        """Log a failure message with optional indent, separator, and color."""
+        """Log a failure message with optional indent, separator, color, and pprint."""
         if self.isEnabledFor(FAIL):
             self._log_with_indent(
-                FAIL, message, indent, sep, n_sep, c, *args, **kwargs
+                FAIL, message, indent, sep, n_sep, c, pprint, *args, **kwargs
             )
 
     def to(self, file_path, level=None, mode="w"):

scitex/ml/__init__.py

@@ -11,7 +11,7 @@ Usage:
 """
 
 # Re-export everything from ai module
-from ..ai import *  # noqa: F403,F401
+from scitex.ai import *  # noqa: F403,F401
 
 __all__ = [
     "classification",

scitex/nn/_Filters.py

@@ -36,12 +36,12 @@ import torch
 import torch.nn as nn
 import torch.nn.functional as F
 
-from ..dsp.utils import build_bandpass_filters, init_bandpass_filters
-from ..dsp.utils._ensure_3d import ensure_3d
-from ..dsp.utils._ensure_even_len import ensure_even_len
-from ..dsp.utils._zero_pad import zero_pad
-from ..dsp.utils.filter import design_filter
-from ..gen._to_even import to_even
+from scitex.dsp.utils import build_bandpass_filters, init_bandpass_filters
+from scitex.dsp.utils._ensure_3d import ensure_3d
+from scitex.dsp.utils._ensure_even_len import ensure_even_len
+from scitex.dsp.utils._zero_pad import zero_pad
+from scitex.dsp.utils.filter import design_filter
+from scitex.gen._to_even import to_even
 
 
 class BaseFilter1D(nn.Module):

scitex/nn/_Spectrogram.py

@@ -8,7 +8,7 @@ import torch.nn.functional as F
 import numpy as np
 import matplotlib.pyplot as plt
 import scitex
-from ..decorators import numpy_fn, torch_fn
+from scitex.decorators import numpy_fn, torch_fn
 
 
 class Spectrogram(nn.Module):

scitex/nn/_Wavelet.py

@@ -13,8 +13,8 @@ import numpy as np
 import torch
 import torch.nn as nn
 import torch.nn.functional as F
-from ..gen._to_even import to_even
-from ..gen._to_odd import to_odd
+from scitex.gen._to_even import to_even
+from scitex.gen._to_odd import to_odd
 
 
 class Wavelet(nn.Module):

scitex/pd/_force_df.py

@@ -12,7 +12,7 @@ __DIR__ = os.path.dirname(__FILE__)
 import numpy as np
 import pandas as pd
 
-from ..types import is_listed_X
+from scitex.types import is_listed_X
 
 
 def force_df(data, filler=np.nan):

scitex/plt/README.md

@@ -1580,7 +1580,7 @@ manuscript.generate_submission_package()  # Journal-ready submission
 ## Best Practices
 
 1. **Always use tracking** - It's enabled by default, don't disable it
-2. **Assign unique IDs** - Use the `id` parameter for easy data identification  
+2. **Assign unique IDs** - Use the `id` parameter for easy data identification
 3. **Separate styling from metadata** - Use `set_xyt()` for labels, `set_meta()` for scientific metadata
 4. **Structure experimental details** - Use dictionaries for machine-readable experimental parameters
 5. **Include comprehensive keywords** - Enable AI agents to categorize and process figures automatically
@@ -1590,6 +1590,31 @@ manuscript.generate_submission_package()  # Journal-ready submission
 9. **Use figure-level metadata** - Apply `set_figure_meta()` for multi-panel comprehensive descriptions
 10. **Export YAML for reproducibility** - All metadata automatically preserved for AI agent processing
 
+### ⚠️ File Format Best Practices
+
+**NEVER use JPEG for scientific figures!**
+
+JPEG uses lossy compression that creates visible artifacts around text, lines, and sharp edges.
+
+**Use these formats:**
+- **PNG** ✅ Lossless raster (perfect for figures with text/lines)
+- **PDF** ✅ Vector format (infinite zoom, required by journals)
+- **JPEG** ❌ NEVER for scientific plots (only for photographs)
+
+```python
+# Correct - Publication-ready formats
+scitex.io.save(fig, 'figure.png', dpi=300, auto_crop=True)  # Lossless
+scitex.io.save(fig, 'figure.pdf')                           # Vector
+
+# Wrong - Creates artifacts around text and lines
+# scitex.io.save(fig, 'figure.jpg')  # ❌ NEVER do this!
+```
+
+**Auto-cropping** is enabled by default and preserves:
+- Image quality (PNG: lossless, PDF: vector)
+- DPI metadata (300 DPI for publication)
+- Scitex metadata (version, style, dimensions, padding, etc.)
+
 ### SciTeX Ecosystem Workflow
 ```python
 # Optimal workflow for AI-powered scientific automation