xarray-behave 0.35.1__tar.gz → 0.35.3__tar.gz

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/.github/workflows/publish.yaml

@@ -19,8 +19,9 @@ jobs:
     strategy:
       fail-fast: False
       matrix:
-        python-version: [3.9 , '3.10'] # , '3.11']
+        python-version: [3.9 , '3.10', '3.11']
         os: [ubuntu-latest, windows-latest, macOS-13, macOS-14]
+        # os: [macOS-13, macOS-14]
         # python-version: ['3.11']
         # os: [ubuntu-latest]
     defaults:  # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: xarray-behave
-Version: 0.35.1
+Version: 0.35.3
 Summary: xarray tools for behavioral data.
 Author-email: Jan Clemens <clemensjan@googlemail.com>
 Requires-Python: >3.6

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/conda/xarray-behave/meta.yaml

@@ -35,7 +35,8 @@ requirements:
     - xarray
     - dask
     #- py
-    - conda-forge::pyside6 # [not win]
+    - conda-forge::pyside6 # [linux]
+    - conda-forge::pyside2 # [osx or arm64]
     - pyside6 # [win and py==310]
     - pyside2 # [win and py>310]
     - pyside2 # [win and py==39]

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/__init__.py

@@ -1,5 +1,6 @@
 """xarray tools for behavioral data."""
-__version__ = "0.35.1"
+
+__version__ = "0.35.3"
 
 from .xarray_behave import assemble, assemble_metrics, load, save
 import os

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/annot.py

@@ -2,6 +2,7 @@
 
 TODO: From/to traces
 """
+
 import numpy as np
 import xarray as xr
 import pandas as pd
@@ -132,19 +133,20 @@ class Events(UserDict):
         names = []
         start_seconds = []
         stop_seconds = []
-
         if len(dct.values()):
-            if list(dct.values())[0].shape[1] > 2:
+            # check if there are annotations and if so, if they comes with channel information
+            if list(dct.values())[0].ndim > 1 and list(dct.values())[0].shape[1] > 2:
                 channels = []
             else:
                 channels = None
 
             for k, v in dct.items():
-                names.extend([k] * v.shape[0])
-                start_seconds.extend(v[:, 0])
-                stop_seconds.extend(v[:, 1])
-                if channels is not None:
-                    channels.extend(v[:, 2])
+                if len(v):  # check if there are annotations
+                    names.extend([k] * v.shape[0])
+                    start_seconds.extend(v[:, 0])
+                    stop_seconds.extend(v[:, 1])
+                    if channels is not None:
+                        channels.extend(v[:, 2])
         out = cls.from_lists(names, start_seconds, stop_seconds, channels=channels)
         return out
 

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/event_utils.py

@@ -2,6 +2,7 @@ import logging
 import numpy as np
 import xarray as xr
 import pandas as pd
+import scipy
 
 
 logger = logging.getLogger(__name__)
@@ -182,14 +183,14 @@ def eventtimes_to_traces(ds, event_times):
     return ds
 
 
-def traces_to_eventtimes(traces, event_names, event_categories):
+def traces_to_eventtimes(traces, event_names, event_categories, events_are_binary: bool = True):
     """[summary]
 
     Args:
         traces ([type]): list of numpy arrays with the binary traces for each event/segment
         event_names ([type]): [description]
         event_categories ([type]): [description]
-
+        events_are_binary (bool, True): detect events indices where value is 1.0. Otherwise use scipy.signal.find_peaks.
     Returns:
         [type]: [description]
     """
@@ -202,7 +203,10 @@ def traces_to_eventtimes(traces, event_names, event_categories):
     for event_idx, (event_name, event_category) in enumerate(zip(event_names, event_categories)):
         logger.info(f"   {event_name}")
         if event_category == "event":
-            event_times[event_name] = np.where(traces[event_idx] == 1)[0]
+            if events_are_binary:
+                event_times[event_name] = np.where(traces[event_idx] == 1)[0]
+            else:
+                event_times[event_name], _ = scipy.signal.find_peaks(traces[event_idx])
         elif event_category == "segment":
             tmp = (traces[event_idx] == 1).astype(float)  # makes this more robust
             onsets = np.where(np.diff(tmp) == 1)[0]

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/gui/app.py

@@ -2,6 +2,7 @@
 
 `python -m xarray_behave.ui datename root`
 """
+
 import os
 import sys
 import logging
@@ -2302,14 +2303,6 @@ class PSV(MainWindow):
             f"  Moved {event_name_to_move} from t=[{region.bounds[0]:1.4f}:{region.bounds[1]:1.4f}] to [{new_region[0]:1.4f}:{new_region[1]:1.4f}] seconds."
         )
 
-        mp = self.annot_view.mousePoint.y()
-        if mp > 0 and mp < 1:
-            new_event_idx = int(mp * self.nb_eventtypes)
-            new_event_name = self.event_times.names[new_event_idx]
-            _, old_name, new_name = self.event_times.change_name(new_region[0], new_event_name)
-            if old_name is not None:
-                logger.info(f"  Changed from {old_name} to {new_name}.")
-
         self.update_xy()
 
     def on_position_change_finished(self, position):
@@ -2324,15 +2317,6 @@ class PSV(MainWindow):
         self.event_times.move_time(event_name_to_move, position.position, new_position)
         logger.info(f"  Moved {event_name_to_move} from t={position.position:1.4f} to {new_position:1.4f} seconds.")
 
-        mp = self.annot_view.mousePoint.y()
-        if mp > 0 and mp < 1:
-            new_event_idx = int(mp * self.nb_eventtypes)
-            new_event_name = self.event_times.names[new_event_idx]
-            print(new_event_name)
-            _, old_name, new_name = self.event_times.change_name(new_position, new_event_name, tol=1)
-            if old_name is not None:
-                logger.info(f"  Changed from {old_name} to {new_name}.")
-
         self.update_xy()
 
     def on_position_dragged(self, fly, pos, offset):
@@ -2807,3 +2791,7 @@ def cli():
         logger.getLogger().setLevel(logging.INFO)
 
     defopt.run(main, show_defaults=False)
+
+
+if __name__ == "__main__":
+    main_das()

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/gui/das.py

@@ -8,6 +8,7 @@ import zarr
 import numpy as np
 import pandas as pd
 import librosa
+import scipy
 import h5py
 
 import das.make_dataset as dsm
@@ -408,8 +409,14 @@ def make(
         names = store.attrs["class_names"][1:]  # [1:] ignore the noise class
         types = store.attrs["class_types"][1:]
         for key in store.keys():
-            ann = event_utils.traces_to_eventtimes(store[key]["y"][:, 1:].T, names, types)
-            ann = {k: v / fs for k, v in ann.items()}  # convert indices to seconds
+            ann = event_utils.traces_to_eventtimes(store[key]["y"][:, 1:].T, names, types, events_are_binary=False)
+            for k, v in ann.items():
+                if (
+                    v.ndim == 1
+                ):  # add start/stop seconds for events - traces_to_eventtimes only returns event start times but annot expects both start and end
+                    v = np.stack((v, v)).T
+                v = v / fs  # convert indices to seconds
+                ann[k] = v
             ev = annot.Events.from_dict(ann)
             ev.to_df().to_csv(os.path.join(store.attrs["store_folder"], key, "x_annotations.csv"))
     logger.info("The dataset has been made.")

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/gui/formbuilder.py

@@ -26,6 +26,7 @@ is :py:method:`FormBuilderLayout.add_item()`. Look there if you want to know
 what's supported in the YAML file, what exactly each field type does, or if you
 want to add a new type of supported form field.
 """
+
 # modified from https://sleap.ai/_modules/sleap/gui/formbuilder.html
 import yaml
 from typing import Any, Dict, List, Optional, Union, Text

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/io/audio.py

@@ -5,6 +5,7 @@ should return:
     non_audio_data: np.array[time, samples]
     samplerate: Optional[float]
 """
+
 # [x] daq.h5
 # [x] wav, ....
 # [x] npz, npy

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/io/balltracks.py

@@ -3,6 +3,7 @@
 should return:
     x: pd.DataFrame[frames, (variables)]
 """
+
 import numpy as np
 import pandas as pd
 from .. import io

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/io/movieparams.py

@@ -1,6 +1,7 @@
 """Load parameters for DLP movies
 
 """
+
 import numpy as np
 import pandas as pd
 import h5py

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/io/poses.py

@@ -7,6 +7,7 @@ should return:
     first_pose_frame: int
     last_pose_frame: int
 """
+
 import h5py
 import numpy as np
 import xarray as xr

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/loaders.py

@@ -1,4 +1,5 @@
 """Load files created by various analysis programs created."""
+
 import numpy as np
 import pandas as pd
 import scipy.interpolate

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/metrics.py

@@ -1,4 +1,5 @@
 """Calculate metrics from behavioral data."""
+
 import numpy as np
 import scipy.signal.windows
 

{xarray-behave-0.35.1 → xarray-behave-0.35.3}/src/xarray_behave/xarray_behave.py

@@ -1,4 +1,5 @@
 """Create self-documenting xarray dataset from behavioral recordings and annotations."""
+
 import numpy as np
 from samplestamps.samplestamps import SampStamp, SimpleStamp
 import scipy.interpolate