PyPI - py-neuromodulation - Versions diffs - 0.1.2__py3-none-any.whl → 0.1.4__py3-none-any.whl - Mend

py-neuromodulation 0.1.2py3-none-any.whl → 0.1.4py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (11) hide show

py_neuromodulation/features/sharpwaves.py CHANGED Viewed

@@ -144,8 +144,14 @@ class SharpwaveAnalyzer(NMFeature):
                 )
         self.filter_names = [name for name, _ in self.list_filter]
-        self.filters = np.vstack([filter for _, filter in self.list_filter])
-        self.filters = np.tile(self.filters[None, :, :], (len(self.ch_names), 1, 1))
+        filter_lengths = [len(f) for _, f in self.list_filter]
+        self.equal_filters_lengths = len(set(filter_lengths)) <= 1
+        if self.equal_filters_lengths:
+            self.filters = np.vstack([f for _, f in self.list_filter])
+            self.filters = np.tile(self.filters[None, :, :], (len(self.ch_names), 1, 1))
+        else:
+            self.filters = [np.tile(f, (len(self.ch_names), 1)) for _, f in self.list_filter]
         self.used_features = self.sw_settings.sharpwave_features.get_enabled()
@@ -235,8 +241,14 @@ class SharpwaveAnalyzer(NMFeature):
         from scipy.signal import fftconvolve
-        data = np.tile(data[:, None, :], (1, len(self.list_filter), 1))
-        data = fftconvolve(data, self.filters, axes=2, mode="same")
+        if self.equal_filters_lengths:
+            data = np.tile(data[:, None, :], (1, len(self.list_filter), 1))
+            data = fftconvolve(data, self.filters, axes=2, mode="same")
+        else:
+            len_data = len(data[0])
+            conv_results = [fftconvolve(data, f, mode="same") for f in self.filters]
+            data = np.concat(conv_results, axis=1)
+            data = data.reshape([len(self.ch_names), len(self.filters), len_data])
         self.filtered_data = (
             data  # TONI: Expose filtered data for example 3, need a better way

py_neuromodulation/gui/frontend/assets/{index-_6V8ZfAS.js → index-B53U6dwc.js} RENAMED Viewed

@@ -13906,7 +13906,11 @@ const useSessionStore = createStore("session", (set2, get) => ({
   sourceType: null,
   // 'file' or 'lsl'
   isSourceValid: false,
-  fileSource: {},
+  fileSource: {
+    name: "",
+    path: "",
+    size: 0
+  },
   // FileInfo object
   lslSource: {
     selectedStream: null,
@@ -14183,7 +14187,7 @@ const useSessionStore = createStore("session", (set2, get) => ({
     sourceType: null,
     isSourceValid: false,
     fileSource: {
-      filePath: ""
+      path: ""
     },
     lslSource: {
       streamName: ""

py_neuromodulation/gui/frontend/index.html CHANGED Viewed

@@ -5,7 +5,7 @@
     <link rel="icon" type="image/svg+xml" href="/charite.svg" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>PyNeuromodulation</title>
-    <script type="module" crossorigin src="/assets/index-_6V8ZfAS.js"></script>
+    <script type="module" crossorigin src="/assets/index-B53U6dwc.js"></script>
     <link rel="modulepreload" crossorigin href="/assets/plotly-DTCwMlpS.js">
   </head>
   <body>

py_neuromodulation/lsl_api.cfg CHANGED Viewed

@@ -1,3 +1,3 @@
 [log]
-level = 0
-file = ./lsllog.txt
+level = 6
+file = ./lsllog.txt

py_neuromodulation/stream/stream.py CHANGED Viewed

@@ -39,7 +39,7 @@ class Stream:
         path_grids: _PathLike | None = None,
         coord_names: list | None = None,
         coord_list: list | None = None,
-        verbose: bool = True,
+        verbose: bool = False,
     ) -> None:
         """Stream initialization
@@ -208,6 +208,7 @@ class Stream:
         simulate_real_time: bool = False,
         decoder: RealTimeDecoder | None = None,
         backend_interface: StreamBackendInterface | None = None,
+        delete_ind_batch_files_after_stream: bool = True,
     ) -> "pd.DataFrame":
         self.is_stream_lsl = is_stream_lsl
         self.stream_lsl_name = stream_lsl_name
@@ -240,7 +241,8 @@ class Stream:
             verbose=self.verbose,
         )
-        nm.logger.log_to_file(out_dir)
+        if self.verbose:
+            nm.logger.log_to_file(out_dir)
         self.generator: Iterator
         if not is_stream_lsl and data is not None:
@@ -337,6 +339,9 @@ class Stream:
         self._save_after_stream()
         self.is_running = False
+        if delete_ind_batch_files_after_stream is True:
+            file_writer.delete_ind_files()
         return feature_df  # Timon: We could think of returnader instead
     def _prepare_raw_data_dict(self, data_batch: np.ndarray) -> dict[str, Any]:

py_neuromodulation/utils/file_writer.py CHANGED Viewed

@@ -108,3 +108,11 @@ class MsgPackFileWriter(AbstractFileWriter):
                 with open(outpath, "rb") as f:
                     data = msgpack.unpack(f)
                 data.to_csv(self.csv_path, index=False)
+    def delete_ind_files(self,):
+        """
+        Delete individual MessagePack files.
+        """
+        files_msg_pack = list(self.out_dir.glob(f"{self.name}-*.msgpack"))
+        for file in files_msg_pack:
+            file.unlink()

{py_neuromodulation-0.1.2.dist-info → py_neuromodulation-0.1.4.dist-info}/METADATA RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: py_neuromodulation
-Version: 0.1.2
+Version: 0.1.4
 Summary: Real-time analysis of intracranial neurophysiology recordings.
 Project-URL: Homepage, https://neuromodulation.github.io/py_neuromodulation/
 Project-URL: Documentation, https://neuromodulation.github.io/py_neuromodulation/
@@ -35,7 +35,7 @@ Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.11
+Requires-Python: >=3.12
 Requires-Dist: cbor2>=5.6.4
 Requires-Dist: fastapi
 Requires-Dist: fooof
@@ -48,6 +48,7 @@ Requires-Dist: mne-bids>=0.8
 Requires-Dist: mne-connectivity
 Requires-Dist: mne-lsl>=1.2.0
 Requires-Dist: mrmr-selection
+Requires-Dist: msgpack
 Requires-Dist: msgpack>=1.1.0
 Requires-Dist: nibabel>=5.3.2
 Requires-Dist: nolds>=0.6.1
@@ -59,6 +60,7 @@ Requires-Dist: pyarrow>=14.0.2
 Requires-Dist: pybispectra>=1.2.0
 Requires-Dist: pydantic>=2.7.3
 Requires-Dist: pyparrm
+Requires-Dist: pyqt6
 Requires-Dist: pywebview
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: scikit-optimize
@@ -128,7 +130,7 @@ Find the documentation here neuromodulation.github.io/py_neuromodulation/ for ex
 Installation
 ============
-py_neuromodulation requires at least python 3.10. For installation you can use pip:
+py_neuromodulation requires at least python 3.12. For installation you can use pip:
 .. code-block::
@@ -138,7 +140,7 @@ Alternatively you can also clone the pacakge and install it using `uv <https://d
 .. code-block::
-    uv python install 3.10
+    uv python install 3.12
     uv venv
     . .venv/bin/activate
     uv sync
@@ -168,7 +170,7 @@ Basic Usage
     stream = nm.Stream(sfreq=sfreq, data=data, sampling_rate_features_hz=sampling_rate_features_hz)
     features = stream.run()
-Check the `Usage <https://py-neuromodulation.readthedocs.io/en/latest/usage.html>`_ and `First examples <https://py-neuromodulation.readthedocs.io/en/latest/auto_examples/plot_0_first_demo.html>`_ for further introduction.
+Check the `Usage <https://neuromodulation.github.io/py_neuromodulation/usage.html>`_ and `First examples <https://neuromodulation.github.io/py_neuromodulation/auto_examples/index.html>`_ for further introduction.
 Contact information
 -------------------

{py_neuromodulation-0.1.2.dist-info → py_neuromodulation-0.1.4.dist-info}/RECORD RENAMED Viewed

@@ -2,7 +2,7 @@ py_neuromodulation/__init__.py,sha256=gu0XWs6bzSMJ7JTu8xxFMCPj6TY0nQ6Q0tuBkK7onR
 py_neuromodulation/default_settings.yaml,sha256=tEKmC16yQwy1MFMRI8cdshT8tTdZ35DB5SqqlNWES04,6387
 py_neuromodulation/grid_cortex.tsv,sha256=k2QOkHY1ej3lJ33LD6DOPVlTynzB3s4BYaoQaoUCyYc,643
 py_neuromodulation/grid_subcortex.tsv,sha256=oCQDYLDdYSa1DAI9ybwECfuzWulFzXqKHyf7oZ1oDBM,25842
-py_neuromodulation/lsl_api.cfg,sha256=8j2EMZkPb-T4w3RAXzoDoWL7bwOgk1vMYPYq9Xi0J6o,37
+py_neuromodulation/lsl_api.cfg,sha256=oKJ5S_9mJjLUCuI4i1jZVOOquNebzdCDIMQWv1gwT3U,39
 py_neuromodulation/run_gui.py,sha256=NW6mjSfgNAHoIcFYOD-kebANTvw3UKr470lLplveicI,700
 py_neuromodulation/ConnectivityDecoding/Automated Anatomical Labeling 3 (Rolls 2020).nii,sha256=Sp-cjF_AuT0Tlilb5s8lB14hVgkXJiR2uKMS9nOQOeg,902981
 py_neuromodulation/ConnectivityDecoding/_get_grid_hull.m,sha256=2RPDGotbLsCzDJLFB2JXatJtfOMno9UUBCBnsOuse8A,714
@@ -42,7 +42,7 @@ py_neuromodulation/features/linelength.py,sha256=8BTctvr9Zj8TEK2HLJqi73j_y2Xgt8l
 py_neuromodulation/features/mne_connectivity.py,sha256=lQHLIXmoyDOWf5agmGMLeq1cQLiG6ud-vYf75CpYTVI,4109
 py_neuromodulation/features/nolds.py,sha256=jNCKQlIfmcAhmzjTAJMbFPhRuPtYZF5BDzR4qHlLp1k,3374
 py_neuromodulation/features/oscillatory.py,sha256=KzQQ3EA75G-hJVmL_YBybWTnuNJFZXAM0aBHudr-dvM,7806
-py_neuromodulation/features/sharpwaves.py,sha256=scFp1jMfq7Eq5th2JtwWm51RpGr8ogQHKCatzv5ZINI,17970
+py_neuromodulation/features/sharpwaves.py,sha256=UpNsaD77Kf5wY22cEhQ9WMNxiBVxjxzDfcsVqubYgm0,18562
 py_neuromodulation/filter/__init__.py,sha256=ut1q8daCZoN7lhTKURGpk1X5oKiS3eSNqR7SkZyGDJw,128
 py_neuromodulation/filter/kalman_filter.py,sha256=-aSAq7KcJ8LUjUThsQtTaIcvz-Qtavik6ltk59j7O-Q,2194
 py_neuromodulation/filter/kalman_filter_external.py,sha256=_7FFq-1GQY9mNA0EvmaM4wQ46DVkHC9bYFIgiw9b6nY,61367
@@ -57,9 +57,9 @@ py_neuromodulation/gui/backend/app_socket.py,sha256=QeaD1AKd_F2oPDKtpikgcNL3v9v8
 py_neuromodulation/gui/backend/app_utils.py,sha256=KgnldjqiYosgGGtE7l7LOg-q3_U1Cpz3IlpnkzGuux8,9693
 py_neuromodulation/gui/backend/app_window.py,sha256=eOk4yjx4qIKYKZhyP8MPlnbZx6OF7DjFgyG8rXjo2vY,6207
 py_neuromodulation/gui/frontend/charite.svg,sha256=RlvOSsBUuFKePKjkuadbtI1Yv3zZ41nRbfqfEb0h_88,1112
-py_neuromodulation/gui/frontend/index.html,sha256=KcUTa9J6SDm0TByHx4jONsKg-71Neb4t6OwLXnkPaZY,470
+py_neuromodulation/gui/frontend/index.html,sha256=-30HoBOEmsPAR1QxJj5L4TpPevYgRyf4VIDR4CtpXU4,470
 py_neuromodulation/gui/frontend/assets/Figtree-VariableFont_wght-CkXbWBDP.ttf,sha256=_tZBDRp07GKuFOiGalezi5Pedl29EpNUhoJ2lAspjXA,62868
-py_neuromodulation/gui/frontend/assets/index-_6V8ZfAS.js,sha256=2w7EYZXY-d-YBFdoMyzJyfzIyds27tV2a5y1-X29lcs,13847236
+py_neuromodulation/gui/frontend/assets/index-B53U6dwc.js,sha256=2-GEEs-bOOec81oVIwiLZyQExQW0qvQy3kSHa2DOjQ0,13847275
 py_neuromodulation/gui/frontend/assets/plotly-DTCwMlpS.js,sha256=O34l2pwjKay4L9VvYbEvRUuJ8PbvTTQGaPqZUcoao0g,1696475
 py_neuromodulation/liblsl/libpugixml.so.1.12,sha256=_bCOHUjcnGpDiROg1qjgty8ZQhcKHSnaCIP6SMgw6SY,240248
 py_neuromodulation/liblsl/linux/bionic_amd64/liblsl.1.16.2.so,sha256=YXFbA23CQqWg6mWhk-73WY9gSx79NtgnBr6UFVByC2I,1033592
@@ -91,19 +91,19 @@ py_neuromodulation/stream/generator.py,sha256=UKLuM8gz2YLBuVQnQNkkOOKhwsyW27ZgvR
 py_neuromodulation/stream/mnelsl_player.py,sha256=KksAWzr78JPqPlECweWZ7JThoxmTVWGo1_-m-fEL0N4,6351
 py_neuromodulation/stream/mnelsl_stream.py,sha256=-uHMCNLZwIcjiT9AMGWkJit5GsZjEJYkpki_DoaLzWY,4352
 py_neuromodulation/stream/settings.py,sha256=--K4NOlR3QNmg4ISgtvC1z_Ucf7MvGChvocck3w6LoI,11832
-py_neuromodulation/stream/stream.py,sha256=rpuhBv2W4NyBRy2I8gUoam-8li3oiyd2Ni7TIRHCCu0,16405
+py_neuromodulation/stream/stream.py,sha256=tcIH0tW99qxrMS3GeRF45xe9K3PO6FB8JlYESH5uNDk,16593
 py_neuromodulation/utils/__init__.py,sha256=Ok3STMpsflCTclJC9C1iQgdT-3HNGMM7U45w5Oespr4,46
 py_neuromodulation/utils/channels.py,sha256=bDUZZ8MB3T-Kcs6zI52MUmvC8qx9KAH-F9U0GyND79U,10649
 py_neuromodulation/utils/database.py,sha256=VEFsmbYDQWwaoZKmJCG8oyWoDTbfSiT_p0n7da9_Pn4,4755
-py_neuromodulation/utils/file_writer.py,sha256=rflDqcsRat0uAYppYXf_cYqpodZsyiGvz52JAxxULzg,3187
+py_neuromodulation/utils/file_writer.py,sha256=eJLx3hK1-1VHKFXWHl4bPZH-dJ8zplUBLVQPDOa_VgQ,3427
 py_neuromodulation/utils/io.py,sha256=uE4k3ScspRy_RuWrrV7cdosH4eKxJKAkvnr5KC8SG6A,11515
 py_neuromodulation/utils/keyboard.py,sha256=swoxYhf4Q3pj50EKALUFt6hREfXnoXq2Z2q01IahPe8,1505
 py_neuromodulation/utils/logging.py,sha256=eIBFBRaAMb3KJnoxNFiCkMrTGzWwgfeDs8m5iq6FxN8,2178
 py_neuromodulation/utils/perf.py,sha256=10LYM13iTuWA-il-EMMOyZke3-1gcFEa6WLlHsJLO50,5471
 py_neuromodulation/utils/pydantic_extensions.py,sha256=nkgq8QHeKSJgmf1cBThBLQ9prdeZZ3_Pyeogs-WnHTA,11030
 py_neuromodulation/utils/types.py,sha256=hT4U9uj4PhHfu8cO7xE1oXj_KT1uHtP-rNY_cDbofr0,4643
-py_neuromodulation-0.1.2.dist-info/METADATA,sha256=B8BA9dpSlZjWGHrQYtTt9FFdWAwFQcUKTiGFk_JqRP8,7699
-py_neuromodulation-0.1.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-py_neuromodulation-0.1.2.dist-info/entry_points.txt,sha256=hImSrCn9vJcwocoeehqNyJ-qj5Hgfrg2o6MPAnIaAa0,60
-py_neuromodulation-0.1.2.dist-info/licenses/LICENSE,sha256=EMBwuBRPBo-WkHSjqxZ55E6j95gKNBZ8x30pt-VGfrM,1118
-py_neuromodulation-0.1.2.dist-info/RECORD,,
+py_neuromodulation-0.1.4.dist-info/METADATA,sha256=VHAB6P_4FPz5JZtaJHtI15rXEMRuBbThJX8fKOv8-wE,7733
+py_neuromodulation-0.1.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+py_neuromodulation-0.1.4.dist-info/entry_points.txt,sha256=hImSrCn9vJcwocoeehqNyJ-qj5Hgfrg2o6MPAnIaAa0,60
+py_neuromodulation-0.1.4.dist-info/licenses/LICENSE,sha256=EMBwuBRPBo-WkHSjqxZ55E6j95gKNBZ8x30pt-VGfrM,1118
+py_neuromodulation-0.1.4.dist-info/RECORD,,

{py_neuromodulation-0.1.2.dist-info → py_neuromodulation-0.1.4.dist-info}/WHEEL RENAMED Viewed

File without changes

{py_neuromodulation-0.1.2.dist-info → py_neuromodulation-0.1.4.dist-info}/entry_points.txt RENAMED Viewed

File without changes

{py_neuromodulation-0.1.2.dist-info → py_neuromodulation-0.1.4.dist-info}/licenses/LICENSE RENAMED Viewed

File without changes

py-neuromodulation 0.1.2__py3-none-any.whl → 0.1.4__py3-none-any.whl

py-neuromodulation 0.1.2py3-none-any.whl → 0.1.4py3-none-any.whl