scitex 2.8.1__py3-none-any.whl → 2.10.0__py3-none-any.whl

scitex/dsp/example.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-04-06 01:36:18 (ywatanabe)"
 
 import matplotlib
@@ -9,6 +8,17 @@ import matplotlib.pyplot as plt
 import pandas as pd
 import scitex
 
+import scitex
+
+# Module-level constants (defaults for example functions)
+TGT_FS = 512
+LOW_HZ = 20
+HIGH_HZ = 50
+SIGMA = 10
+
+# Default color cycle
+CC = {"blue": "#1f77b4", "red": "#d62728", "green": "#2ca02c"}
+
 
 # Functions
 def calc_norm_resample_filt_hilbert(xx, tt, fs, sig_type, verbose=True):
@@ -17,18 +27,19 @@ def calc_norm_resample_filt_hilbert(xx, tt, fs, sig_type, verbose=True):
     if sig_type == "tensorpac":
         xx = xx[:, :, 0]
 
-    sigs[f"orig"] = (xx, tt, fs)
+    sigs["orig"] = (xx, tt, fs)
 
     # Normalization
     sigs["z_normed"] = (scitex.dsp.norm.z(xx), tt, fs)
     sigs["minmax_normed"] = (scitex.dsp.norm.minmax(xx), tt, fs)
 
     # Resampling
-    sigs["resampled"] = (
-        scitex.dsp.resample(xx, fs, TGT_FS),
-        tt[:: int(fs / TGT_FS)],
-        TGT_FS,
-    )
+    resampled_xx = scitex.dsp.resample(xx, fs, TGT_FS)
+    # Create proper time vector for resampled signal
+    import numpy as np
+
+    resampled_tt = np.linspace(tt[0], tt[-1], resampled_xx.shape[-1])
+    sigs["resampled"] = (resampled_xx, resampled_tt, TGT_FS)
 
     # Noise injection
     sigs["gaussian_noise_added"] = (scitex.dsp.add_noise.gauss(xx), tt, fs)
@@ -36,15 +47,16 @@ def calc_norm_resample_filt_hilbert(xx, tt, fs, sig_type, verbose=True):
     sigs["pink_noise_added"] = (scitex.dsp.add_noise.pink(xx), tt, fs)
     sigs["brown_noise_added"] = (scitex.dsp.add_noise.brown(xx), tt, fs)
 
-    # Filtering
+    # Filtering (bands format is [[low_hz, high_hz]])
+    bands = [[LOW_HZ, HIGH_HZ]]
     sigs[f"bandpass_filted ({LOW_HZ} - {HIGH_HZ} Hz)"] = (
-        scitex.dsp.filt.bandpass(xx, fs, low_hz=LOW_HZ, high_hz=HIGH_HZ),
+        scitex.dsp.filt.bandpass(xx, fs, bands),
         tt,
         fs,
     )
 
     sigs[f"bandstop_filted ({LOW_HZ} - {HIGH_HZ} Hz)"] = (
-        scitex.dsp.filt.bandstop(xx, fs, low_hz=LOW_HZ, high_hz=HIGH_HZ),
+        scitex.dsp.filt.bandstop(xx, fs, bands),
         tt,
         fs,
     )
@@ -88,18 +100,19 @@ def plot_signals(plt, sigs, sig_type):
         # if sig_type == "tensorpac":
         #     xx = xx[:, :, 0]
 
-        try:
-            ax.plot(
-                tt,
-                xx[i_batch, i_ch],
-                label=col,
-                c=CC["red"] if col == "hilbert_amp" else CC["blue"],
-            )
-        except Exception as e:
-            print(e)
-            import ipdb
-
-            ipdb.set_trace()
+        # Handle potential shape mismatches from filter operations
+        signal = xx[i_batch, i_ch]
+        if hasattr(signal, "squeeze"):
+            signal = signal.squeeze()
+        if hasattr(signal, "numpy"):
+            signal = signal.numpy()
+
+        ax.plot(
+            tt,
+            signal,
+            label=col,
+            c=CC["red"] if col == "hilbert_amp" else CC["blue"],
+        )
 
         # Adjustments
         ax.legend(loc="upper left")

scitex/dsp/filt.py

@@ -1,11 +1,10 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-04 02:05:47 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/dsp/filt.py
 
-import scitex
 import numpy as np
 
+import scitex
 from scitex.decorators import signal_fn
 
 # No top-level imports from nn module to avoid circular dependency
@@ -24,6 +23,8 @@ def bandpass(x, fs, bands, t=None):
     import torch
     from scitex.nn._Filters import BandPassFilter
 
+    from scitex.nn._Filters import BandPassFilter
+
     # Convert bands to tensor if it's not already
     if not isinstance(bands, torch.Tensor):
         bands = torch.tensor(bands, dtype=torch.float32)
@@ -32,8 +33,13 @@ def bandpass(x, fs, bands, t=None):
 
 @signal_fn
 def bandstop(x, fs, bands, t=None):
+    import torch
+
     from scitex.nn._Filters import BandStopFilter
 
+    # Convert bands to tensor if it's not already
+    if not isinstance(bands, torch.Tensor):
+        bands = torch.tensor(bands, dtype=torch.float32)
     return BandStopFilter(bands, fs, x.shape[-1])(x, t=t)
 
 
@@ -59,7 +65,6 @@ if __name__ == "__main__":
     import sys
 
     import matplotlib.pyplot as plt
-    import torch
 
     # Start
     CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(sys, plt)

scitex/dsp/reference.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "ywatanabe (2024-11-02 22:48:44)"
 # File: ./scitex_repo/src/scitex/dsp/reference.py
 
 import torch as _torch
+
 from scitex.decorators import torch_fn as _torch_fn
 
 
@@ -29,7 +29,8 @@ def random(x, dim=-2):
 def take_reference(x, tgt_indi, dim=-2):
     idx_all = [slice(None)] * x.ndim
     idx_all[dim] = tgt_indi
-    re_referenced = x - x[tgt_indi]
+    ref = x[tuple(idx_all)].unsqueeze(dim)
+    re_referenced = x - ref
     assert x.shape == re_referenced.shape
     return re_referenced
 

scitex/dsp/utils/__init__.py

@@ -7,9 +7,10 @@ from ._differential_bandpass_filters import (
 )
 from ._ensure_3d import ensure_3d
 from ._ensure_even_len import ensure_even_len
-from ._zero_pad import zero_pad
+from ._zero_pad import _zero_pad_1d, zero_pad
 
 __all__ = [
+    "_zero_pad_1d",
     "build_bandpass_filters",
     "ensure_3d",
     "ensure_even_len",

scitex/dsp/utils/_differential_bandpass_filters.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-26 22:24:13 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/dsp/utils/_differential_bandpass_filters.py
 
@@ -18,8 +17,16 @@ from scitex.gen._to_odd import to_odd
 
 try:
     from torchaudio.prototype.functional import sinc_impulse_response
-except:
-    pass
+except ImportError:
+    sinc_impulse_response = None
+
+
+def _check_sinc_available():
+    if sinc_impulse_response is None:
+        raise ImportError(
+            "sinc_impulse_response requires torchaudio.prototype.functional. "
+            "Install torchaudio with: pip install torchaudio"
+        )
 
 
 # Functions
@@ -35,6 +42,7 @@ def init_bandpass_filters(
     amp_n_bands=50,
     cycle=3,
 ):
+    _check_sinc_available()
     # Learnable parameters
     pha_mids = nn.Parameter(torch.linspace(pha_low_hz, pha_high_hz, pha_n_bands))
     amp_mids = nn.Parameter(torch.linspace(amp_low_hz, amp_high_hz, amp_n_bands))
@@ -44,13 +52,15 @@ def init_bandpass_filters(
 
 @torch_fn
 def build_bandpass_filters(sig_len, fs, pha_mids, amp_mids, cycle):
+    _check_sinc_available()
+
     def _define_freqs(mids, factor):
         lows = mids - mids / factor
         highs = mids + mids / factor
         return lows, highs
 
     def define_order(low_hz, fs, sig_len, cycle):
-        order = cycle * int((fs // low_hz))
+        order = cycle * int(fs // low_hz)
         order = order if 3 * order >= sig_len else (sig_len - 1) // 3
         order = to_even(order)
         return order

scitex/dt/__init__.py

@@ -1,8 +1,45 @@
 #!/usr/bin/env python3
-"""Scitex dt module."""
+# Timestamp: "2026-01-05 14:40:00 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/dt/__init__.py
 
-from ._linspace import linspace
+"""
+Scitex dt module - alias for scitex.datetime.
+
+This module is an alias for scitex.datetime, providing a shorter name
+for convenience. Both modules are fully supported.
+
+Usage:
+    from scitex import dt
+    dt.linspace(...)
+
+    # Equivalent to:
+    from scitex import datetime
+    datetime.linspace(...)
+"""
+
+# Re-export everything from datetime module
+from scitex.datetime import (
+    ALTERNATIVE_FORMATS,
+    STANDARD_FORMAT,
+    format_for_display,
+    format_for_filename,
+    get_time_delta_seconds,
+    linspace,
+    normalize_timestamp,
+    parse_patient_recording_start_format,
+    to_datetime,
+    validate_timestamp_format,
+)
 
 __all__ = [
     "linspace",
+    "normalize_timestamp",
+    "to_datetime",
+    "format_for_filename",
+    "format_for_display",
+    "validate_timestamp_format",
+    "get_time_delta_seconds",
+    "parse_patient_recording_start_format",
+    "STANDARD_FORMAT",
+    "ALTERNATIVE_FORMATS",
 ]