scitex 2.10.3__py3-none-any.whl → 2.13.0__py3-none-any.whl

scitex/dsp/_demo_sig.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-06 01:45:32 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/dsp/_demo_sig.py
 
@@ -8,12 +7,35 @@ import sys
 import warnings
 
 import matplotlib.pyplot as plt
-import mne
 import numpy as np
-from mne.datasets import sample
-from ripple_detection.simulate import simulate_LFP, simulate_time
 from scipy.signal import chirp
-from tensorpac.signals import pac_signals_wavelet
+
+try:
+    import mne
+    from mne.datasets import sample
+
+    MNE_AVAILABLE = True
+except ImportError:
+    MNE_AVAILABLE = False
+    mne = None
+    sample = None
+
+try:
+    from ripple_detection.simulate import simulate_LFP, simulate_time
+
+    RIPPLE_DETECTION_AVAILABLE = True
+except ImportError:
+    RIPPLE_DETECTION_AVAILABLE = False
+    simulate_LFP = None
+    simulate_time = None
+
+try:
+    from tensorpac.signals import pac_signals_wavelet
+
+    TENSORPAC_AVAILABLE = True
+except ImportError:
+    TENSORPAC_AVAILABLE = False
+    pac_signals_wavelet = None
 
 from scitex.io._load_configs import load_configs
 
@@ -21,6 +43,27 @@ from scitex.io._load_configs import load_configs
 CONFIG = load_configs(verbose=False)
 
 
+def _check_mne():
+    if not MNE_AVAILABLE:
+        raise ImportError(
+            "MNE-Python is not installed. Please install with: pip install mne"
+        )
+
+
+def _check_ripple_detection():
+    if not RIPPLE_DETECTION_AVAILABLE:
+        raise ImportError(
+            "ripple_detection is not installed. Please install with: pip install ripple_detection"
+        )
+
+
+def _check_tensorpac():
+    if not TENSORPAC_AVAILABLE:
+        raise ImportError(
+            "tensorpac is not installed. Please install with: pip install tensorpac"
+        )
+
+
 # Functions
 def demo_sig(
     sig_type="periodic",
@@ -207,6 +250,7 @@ def _demo_sig_tensorpac(
     n_segments=20,
     verbose=False,
 ):
+    _check_tensorpac()
     n_times = int(t_sec * fs)
     x_2d, tt = pac_signals_wavelet(
         sf=fs,
@@ -222,6 +266,7 @@ def _demo_sig_tensorpac(
 
 
 def _demo_sig_meg(batch_size=8, n_chs=19, t_sec=10, fs=512, verbose=False, **kwargs):
+    _check_mne()
     data_path = sample.data_path()
     meg_path = data_path / "MEG" / "sample"
     raw_fname = meg_path / "sample_audvis_raw.fif"
@@ -280,6 +325,7 @@ def _demo_sig_chirp_1d(
 
 
 def _demo_sig_ripple_1d(t_sec=10, fs=512, **kwargs):
+    _check_ripple_detection()
     n_samples = t_sec * fs
     t = simulate_time(n_samples, fs)
     n_ripples = random.randint(1, 5)

scitex/dsp/_mne.py

@@ -1,14 +1,25 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-04 02:07:36 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/dsp/_mne.py
 
-import mne
+try:
+    import mne
+
+    MNE_AVAILABLE = True
+except ImportError:
+    MNE_AVAILABLE = False
+    mne = None
+
 import pandas as pd
+
 from .params import EEG_MONTAGE_1020
 
 
 def get_eeg_pos(channel_names=EEG_MONTAGE_1020):
+    if not MNE_AVAILABLE:
+        raise ImportError(
+            "MNE-Python is not installed. Please install with: pip install mne"
+        )
     # Load the standard 10-20 montage
     standard_montage = mne.channels.make_standard_montage("standard_1020")
     standard_montage.ch_names = [

scitex/dsp/_modulation_index.py

@@ -1,12 +1,19 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-04 02:09:55 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/dsp/_modulation_index.py
 
-import torch
+try:
+    import torch
+
+    TORCH_AVAILABLE = True
+except ImportError:
+    TORCH_AVAILABLE = False
+    torch = None
 
 from scitex.decorators import signal_fn
-from scitex.nn._ModulationIndex import ModulationIndex
+
+if TORCH_AVAILABLE:
+    from scitex.nn._ModulationIndex import ModulationIndex
 
 
 @signal_fn
@@ -15,6 +22,10 @@ def modulation_index(pha, amp, n_bins=18, amp_prob=False):
     pha: (batch_size, n_chs, n_freqs_pha, n_segments, seq_len)
     amp: (batch_size, n_chs, n_freqs_amp, n_segments, seq_len)
     """
+    if not TORCH_AVAILABLE:
+        raise ImportError(
+            "PyTorch is not installed. Please install with: pip install torch"
+        )
     return ModulationIndex(n_bins=n_bins, amp_prob=amp_prob)(pha, amp)
 
 
@@ -32,6 +43,7 @@ if __name__ == "__main__":
     import sys
 
     import matplotlib.pyplot as plt
+
     import scitex
 
     # Start

scitex/dsp/_pac.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-26 22:24:40 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/dsp/_pac.py
 
@@ -9,11 +8,28 @@ import sys
 
 import matplotlib.pyplot as plt
 import numpy as np
-import torch
-from scitex.str import printc
 
-from scitex.decorators import signal_fn, batch_fn
-from scitex.nn._PAC import PAC
+try:
+    import torch
+
+    TORCH_AVAILABLE = True
+except ImportError:
+    TORCH_AVAILABLE = False
+    torch = None
+
+
+from scitex.decorators import signal_fn
+
+if TORCH_AVAILABLE:
+    from scitex.nn._PAC import PAC
+
+
+def _check_torch():
+    if not TORCH_AVAILABLE:
+        raise ImportError(
+            "PyTorch is not installed. Please install with: pip install torch"
+        )
+
 
 """
 scitex.dsp.pac function
@@ -66,6 +82,7 @@ def pac(
         )
         pac, pha_mids_hz, amp_mids_hz = scitex.dsp.pac(xx, fs)
     """
+    _check_torch()
 
     def process_ch_batching(m, x, batch_size_ch, device):
         n_chs = x.shape[1]
@@ -107,6 +124,7 @@ def pac(
 
 if __name__ == "__main__":
     import matplotlib.pyplot as plt
+
     import scitex
 
     # Start

scitex/dsp/_psd.py

@@ -1,14 +1,21 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-04 02:11:25 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/dsp/_psd.py
 
 """This script does XYZ."""
 
-import torch
+try:
+    import torch
+
+    TORCH_AVAILABLE = True
+except ImportError:
+    TORCH_AVAILABLE = False
+    torch = None
 
 from scitex.decorators import signal_fn
-from scitex.nn._PSD import PSD
+
+if TORCH_AVAILABLE:
+    from scitex.nn._PSD import PSD
 
 
 @signal_fn
@@ -32,6 +39,10 @@ def psd(
     ax.ylabel("log(Power [uV^2 / Hz]) [a.u.]")
     plt.show()
     """
+    if not TORCH_AVAILABLE:
+        raise ImportError(
+            "PyTorch is not installed. Please install with: pip install torch"
+        )
     psd, freqs = PSD(fs, prob=prob, dim=dim)(x)
     return psd, freqs
 
@@ -59,10 +70,11 @@ def band_powers(self, psd):
 
 if __name__ == "__main__":
     import sys
-    import scitex
 
     import matplotlib.pyplot as plt
 
+    import scitex
+
     # Start
     CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(sys, plt)
 

scitex/dsp/_resample.py

@@ -1,16 +1,36 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-04-13 02:35:11 (ywatanabe)"
 
+try:
+    import torch
+
+    TORCH_AVAILABLE = True
+except ImportError:
+    TORCH_AVAILABLE = False
+    torch = None
+
+try:
+    import torchaudio.transforms as T
+
+    TORCHAUDIO_AVAILABLE = True
+except ImportError:
+    TORCHAUDIO_AVAILABLE = False
+    T = None
 
-import torch
-import torchaudio.transforms as T
-from scitex.decorators import signal_fn
 import scitex
+from scitex.decorators import signal_fn
 
 
 @signal_fn
 def resample(x, src_fs, tgt_fs, t=None):
+    if not TORCH_AVAILABLE:
+        raise ImportError(
+            "PyTorch is not installed. Please install with: pip install torch"
+        )
+    if not TORCHAUDIO_AVAILABLE:
+        raise ImportError(
+            "torchaudio is not installed. Please install with: pip install torchaudio"
+        )
     xr = T.Resample(src_fs, tgt_fs, dtype=x.dtype).to(x.device)(x)
     if t is None:
         return xr

scitex/dsp/_transform.py

@@ -1,16 +1,29 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-04-08 12:41:59 (ywatanabe)"#!/usr/bin/env python3
 
 
-import warnings
 
 import numpy as np
 import pandas as pd
-import torch
+
+try:
+    import torch
+
+    TORCH_AVAILABLE = True
+except ImportError:
+    TORCH_AVAILABLE = False
+    torch = None
+
 from scitex.decorators import torch_fn
 
 
+def _check_torch():
+    if not TORCH_AVAILABLE:
+        raise ImportError(
+            "PyTorch is not installed. Please install with: pip install torch"
+        )
+
+
 def to_sktime_df(arr):
     """
     Convert a 3D numpy array into a DataFrame suitable for sktime.

scitex/dsp/add_noise.py

@@ -2,12 +2,26 @@
 # Time-stamp: "ywatanabe (2024-11-02 23:09:49)"
 # File: ./scitex_repo/src/scitex/dsp/add_noise.py
 
-import torch
+try:
+    import torch
+
+    TORCH_AVAILABLE = True
+except ImportError:
+    TORCH_AVAILABLE = False
+    torch = None
 
 from scitex.decorators import signal_fn
 
 
+def _check_torch():
+    if not TORCH_AVAILABLE:
+        raise ImportError(
+            "PyTorch is not installed. Please install with: pip install torch"
+        )
+
+
 def _uniform(shape, amp=1.0):
+    _check_torch()
     a, b = -amp, amp
     return -amp + (2 * amp) * torch.rand(shape)
 

scitex/dsp/norm.py

@@ -1,18 +1,33 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-04-05 12:15:42 (ywatanabe)"
 
-import torch as _torch
+try:
+    import torch as _torch
+
+    TORCH_AVAILABLE = True
+except ImportError:
+    TORCH_AVAILABLE = False
+    _torch = None
+
 from scitex.decorators import signal_fn as _signal_fn
 
 
+def _check_torch():
+    if not TORCH_AVAILABLE:
+        raise ImportError(
+            "PyTorch is not installed. Please install with: pip install torch"
+        )
+
+
 @_signal_fn
 def z(x, dim=-1):
+    _check_torch()
     return (x - x.mean(dim=dim, keepdim=True)) / x.std(dim=dim, keepdim=True)
 
 
 @_signal_fn
 def minmax(x, amp=1.0, dim=-1, fn="mean"):
+    _check_torch()
     MM = x.max(dim=dim, keepdims=True)[0].abs()
     mm = x.min(dim=dim, keepdims=True)[0].abs()
     return amp * x / _torch.maximum(MM, mm)

scitex/dsp/reference.py

@@ -2,13 +2,27 @@
 # Time-stamp: "ywatanabe (2024-11-02 22:48:44)"
 # File: ./scitex_repo/src/scitex/dsp/reference.py
 
-import torch as _torch
+try:
+    import torch as _torch
+
+    TORCH_AVAILABLE = True
+except ImportError:
+    TORCH_AVAILABLE = False
+    _torch = None
 
 from scitex.decorators import torch_fn as _torch_fn
 
 
+def _check_torch():
+    if not TORCH_AVAILABLE:
+        raise ImportError(
+            "PyTorch is not installed. Please install with: pip install torch"
+        )
+
+
 @_torch_fn
 def common_average(x, dim=-2):
+    _check_torch()
     re_referenced = (x - x.mean(dim=dim, keepdims=True)) / x.std(dim=dim, keepdims=True)
     assert x.shape == re_referenced.shape
     return re_referenced
@@ -16,6 +30,7 @@ def common_average(x, dim=-2):
 
 @_torch_fn
 def random(x, dim=-2):
+    _check_torch()
     idx_all = [slice(None)] * x.ndim
     idx_rand_dim = _torch.randperm(x.shape[dim])
     idx_all[dim] = idx_rand_dim
@@ -27,6 +42,7 @@ def random(x, dim=-2):
 
 @_torch_fn
 def take_reference(x, tgt_indi, dim=-2):
+    _check_torch()
     idx_all = [slice(None)] * x.ndim
     idx_all[dim] = tgt_indi
     ref = x[tuple(idx_all)].unsqueeze(dim)

scitex/dsp/utils/_differential_bandpass_filters.py

@@ -8,8 +8,16 @@ import sys
 
 import matplotlib.pyplot as plt
 import numpy as np
-import torch
-import torch.nn as nn
+
+try:
+    import torch
+    import torch.nn as nn
+
+    TORCH_AVAILABLE = True
+except ImportError:
+    TORCH_AVAILABLE = False
+    torch = None
+    nn = None
 
 from scitex.decorators import torch_fn
 from scitex.gen._to_even import to_even
@@ -17,10 +25,20 @@ from scitex.gen._to_odd import to_odd
 
 try:
     from torchaudio.prototype.functional import sinc_impulse_response
+
+    TORCHAUDIO_AVAILABLE = True
 except ImportError:
+    TORCHAUDIO_AVAILABLE = False
     sinc_impulse_response = None
 
 
+def _check_torch():
+    if not TORCH_AVAILABLE:
+        raise ImportError(
+            "PyTorch is not installed. Please install with: pip install torch"
+        )
+
+
 def _check_sinc_available():
     if sinc_impulse_response is None:
         raise ImportError(

scitex/dsp/utils/_zero_pad.py

@@ -1,18 +1,32 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Time-stamp: "2024-11-26 10:30:34 (ywatanabe)"
 # File: ./scitex_repo/src/scitex/dsp/utils/_zero_pad.py
 
 THIS_FILE = "/home/ywatanabe/proj/scitex_repo/src/scitex/dsp/utils/_zero_pad.py"
 
 import numpy as np
-import torch
-import torch.nn.functional as F
-from scitex.decorators import torch_fn
+
+try:
+    import torch
+    import torch.nn.functional as F
+
+    TORCH_AVAILABLE = True
+except ImportError:
+    TORCH_AVAILABLE = False
+    torch = None
+    F = None
+
+
+def _check_torch():
+    if not TORCH_AVAILABLE:
+        raise ImportError(
+            "PyTorch is not installed. Please install with: pip install torch"
+        )
 
 
 def _zero_pad_1d(x, target_length):
     """Zero pad a 1D tensor to target length."""
+    _check_torch()
     if not isinstance(x, torch.Tensor):
         x = torch.tensor(x)
     padding_needed = target_length - len(x)

scitex/dt/_normalize_timestamp.py

@@ -408,7 +408,7 @@ def run_main() -> None:
 
     args = parse_args()
 
-    CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
+    CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
         sys,
         plt,
         args=args,

scitex/git/_session.py

@@ -32,7 +32,7 @@ def run_with_session(parse_args_func, main_func):
 
     args = parse_args_func()
 
-    CONFIG, sys.stdout, sys.stderr, plt_obj, CC, rng_manager = stx.session.start(
+    CONFIG, sys.stdout, sys.stderr, plt_obj, CC, rng = stx.session.start(
         sys,
         plt,
         args=args,

scitex/io/__init__.py

@@ -9,21 +9,19 @@ __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 """Scitex IO module with lazy imports to avoid circular dependencies.
 
-Bundle I/O is handled via scitex.fts:
-    from scitex.fts import FTS
-    bundle = FTS("Figure1.stx")
+Bundle I/O is handled via scitex.io.bundle:
+    from scitex.io.bundle import Bundle
+    bundle = Bundle("Figure1.figure")
     bundle.save()
 """
 
 # Import commonly used functions directly
+# Bundle I/O - import the bundle submodule
+from . import bundle
 from ._cache import cache
 from ._flush import flush
 from ._glob import glob, parse_glob
 from ._load import load
-
-# Bundle I/O - import the bundle submodule
-from . import bundle
-
 from ._load_configs import load_configs
 from ._reload import reload
 from ._save import save
@@ -45,20 +43,10 @@ except ImportError:
     has_zarr_key = None
 
 # Import load cache control functions
-from ._load_cache import (
-    clear_cache as clear_load_cache,
-)
-from ._load_cache import (
-    configure_cache,
-    get_cache_info,
-)
+from ._load_cache import clear_cache as clear_load_cache
+from ._load_cache import configure_cache, get_cache_info
 
 # Import load cache control functions
-from ._load_cache import (
-    get_cache_info,
-    configure_cache,
-    clear_cache as clear_load_cache,
-)
 
 # Import save module functions
 try:

scitex/io/_load.py

@@ -16,11 +16,7 @@ from typing import Any, Union
 
 from scitex.decorators import preserve_doc
 
-from ._load_cache import (
-    cache_data,
-    get_cached_data,
-    load_npy_cached,
-)
+from ._load_cache import cache_data, get_cached_data, load_npy_cached
 
 # Core loaders (no special dependencies)
 from ._load_modules._bibtex import _load_bibtex
@@ -101,7 +97,7 @@ except ImportError:
 
 
 def _load_bundle(lpath, verbose=False, **kwargs):
-    """Load a .pltz, .figz, or .statsz bundle.
+    """Load a .plot, .figure, or .stats bundle.
 
     Parameters
     ----------
@@ -114,12 +110,12 @@ def _load_bundle(lpath, verbose=False, **kwargs):
 
     Returns
     -------
-    For .pltz bundles:
+    For .plot bundles:
         tuple: (fig, ax, data) where fig is reconstructed figure,
                ax is the axes, data is DataFrame or None.
-    For .figz bundles:
+    For .figure bundles:
         dict: Figure data with 'spec' and 'panels'.
-    For .statsz bundles:
+    For .stats bundles:
         dict: Stats data with 'spec' and 'comparisons'.
     """
     from .bundle import BundleType
@@ -128,8 +124,8 @@ def _load_bundle(lpath, verbose=False, **kwargs):
     bundle = load_bundle(lpath)
     bundle_type = bundle.get("type")
 
-    if bundle_type == BundleType.PLTZ:
-        # Return (fig, ax, data) tuple for .pltz bundles
+    if bundle_type == BundleType.PLOT:
+        # Return (fig, ax, data) tuple for .plot bundles
         # Note: We return the spec and data, not a reconstructed figure
         # as matplotlib figures cannot be perfectly serialized/deserialized
         from pathlib import Path
@@ -177,19 +173,19 @@ def _load_bundle(lpath, verbose=False, **kwargs):
                 if theme:
                     fig._scitex_theme = theme.get("mode")
 
-            # Data from bundle (merged in load_layered_pltz_bundle)
+            # Data from bundle (merged in load_layered_plot_bundle)
             data = bundle.get("data")
             return fig, ax, data
         else:
             # No PNG, return spec and data
             return bundle.get("spec"), None, bundle.get("data")
 
-    elif bundle_type == BundleType.FIGZ:
-        # Return figure dict for .figz bundles
+    elif bundle_type == BundleType.FIGURE:
+        # Return figure dict for .figure bundles
         return bundle
 
-    elif bundle_type == BundleType.STATSZ:
-        # Return stats dict for .statsz bundles
+    elif bundle_type == BundleType.STATS:
+        # Return stats dict for .stats bundles
         return bundle
 
     return bundle
@@ -300,10 +296,10 @@ def load(
         if verbose:
             print(f"[DEBUG] After Path conversion: {lpath}")
 
-    # Handle bundle formats (.pltz, .figz, .statsz and their .d variants)
-    bundle_extensions = (".figz", ".pltz", ".statsz")
+    # Handle bundle formats (.plot, .figure, .stats and their ZIP variants)
+    bundle_extensions = (".figure", ".plot", ".stats")
     for bext in bundle_extensions:
-        if lpath.endswith(bext) or lpath.endswith(f"{bext}.d"):
+        if lpath.endswith(bext) or lpath.endswith(f"{bext}.zip"):
             return _load_bundle(lpath, verbose=verbose, **kwargs)
 
     # Check if it's a glob pattern