xarray-behave 0.35.2__tar.gz → 0.35.4__tar.gz

{xarray-behave-0.35.2 → xarray-behave-0.35.4}/.github/workflows/publish.yaml

@@ -19,11 +19,11 @@ jobs:
     strategy:
       fail-fast: False
       matrix:
-        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]
+        python-version: ['3.10']
+        os: [ubuntu-latest, windows-latest, macOS-13, macOS-14]
+        include:
+        - python-version: 3.9
+          os: windows-latest
     defaults:  # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
       run:
         shell: bash -l {0}

{xarray-behave-0.35.2 → xarray-behave-0.35.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: xarray-behave
-Version: 0.35.2
+Version: 0.35.4
 Summary: xarray tools for behavioral data.
 Author-email: Jan Clemens <clemensjan@googlemail.com>
 Requires-Python: >3.6

{xarray-behave-0.35.2 → xarray-behave-0.35.4}/conda/xarray-behave/meta.yaml

@@ -16,6 +16,7 @@ requirements:
   host:
     - python {{ python }}
     - pip
+    - numpy=1.23
   run:
     - python {{ python }}
     - defopt=6.3
@@ -24,30 +25,27 @@ requirements:
     - h5py
     - librosa>0.8
     - matplotlib
-    - matplotlib-scalebar
     - pandas
     - scipy>=1.9
     - peakutils
     - pyyaml
     - scikit-learn
     - zarr
-    - numba # >=0.56
+    - numba
     - xarray
     - dask
-    #- py
-    - 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]
-    - pyqtgraph>0.12.2
+    - conda-forge::pyside2
+    # - conda-forge::pyside2 # [linux or osx or arm64]
+    # - conda-forge::pyside6 # [win and py>39]
+    # - conda-forge::pyside2 # [osx or arm64]
+    # - pyside2 # [win and py==39]
+    - pyqtgraph>0.12
     - qtpy
     - superqt
     - rich
     - colorcet
     - python-sounddevice
     - scikit-image
-    # - opencv
     - ffmpeg
     - pyvideoreader
     - samplestamps>=0.6

{xarray-behave-0.35.2 → xarray-behave-0.35.4}/src/xarray_behave/__init__.py

@@ -1,5 +1,6 @@
 """xarray tools for behavioral data."""
-__version__ = "0.35.2"
+
+__version__ = "0.35.4"
 
 from .xarray_behave import assemble, assemble_metrics, load, save
 import os

{xarray-behave-0.35.2 → xarray-behave-0.35.4}/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
@@ -166,7 +167,9 @@ class Events(UserDict):
             columns.append("channel")
         return pd.DataFrame(columns=columns)
 
-    def _append_row(self, df: pd.DataFrame, name: str, start_seconds: float, stop_seconds: Optional[float] = None, channel: int = -1):
+    def _append_row(
+        self, df: pd.DataFrame, name: str, start_seconds: float, stop_seconds: Optional[float] = None, channel: int = -1
+    ):
         if stop_seconds is None:
             stop_seconds = start_seconds
 
@@ -195,12 +198,16 @@ class Events(UserDict):
         """
         df = self._init_df()
         for name in self.names:
-            for start_second, stop_second, channel in zip(self.start_seconds(name), self.stop_seconds(name), self.channels(name)):
+            for start_second, stop_second, channel in zip(
+                self.start_seconds(name), self.stop_seconds(name), self.channels(name)
+            ):
                 df = self._append_row(df, name, start_second, stop_second, channel)
         if preserve_empty:  # ensure we keep events without annotations
             for name, cat in zip(self.names, self.categories.values()):
                 if name not in df.name.values:
-                    stop_seconds = np.nan if cat == "event" else 0  # (np.nan, np.nan) -> empty events, (np.nan, some number) -> empty segments
+                    stop_seconds = (
+                        np.nan if cat == "event" else 0
+                    )  # (np.nan, np.nan) -> empty events, (np.nan, some number) -> empty segments
                     df = self._append_row(df, name, start_seconds=np.nan, stop_seconds=stop_seconds)
         # make sure start and stop seconds are numeric
         df["start_seconds"] = pd.to_numeric(df["start_seconds"], errors="coerce")
@@ -310,7 +317,9 @@ class Events(UserDict):
             name = None
         return name
 
-    def _get_index_of_nearest(self, time: float, name: str, tol: float = 0, min_time: Optional[float] = None, max_time: Optional[float] = None):
+    def _get_index_of_nearest(
+        self, time: float, name: str, tol: float = 0, min_time: Optional[float] = None, max_time: Optional[float] = None
+    ):
         within_range_indices = self.select_range(name, min_time, max_time, strict=False)
         if len(within_range_indices):
             nearest_start = self._find_nearest(self.start_seconds(name)[within_range_indices], time)
@@ -338,9 +347,9 @@ class Events(UserDict):
                 event_at_time = matching_start < time
         elif self.categories[name] == "event":
             if nearest_is_start:
-                event_at_time = np.abs(time - nearest_start) < tol
+                event_at_time = np.abs(time - nearest_start) <= tol
             else:
-                event_at_time = np.abs(time - nearest_stop) < tol
+                event_at_time = np.abs(time - nearest_stop) <= tol
         else:
             event_at_time = False
 
@@ -350,7 +359,13 @@ class Events(UserDict):
             return index
 
     def change_name(
-        self, time: float, new_name: str, tol: float = 0, min_time: Optional[float] = None, max_time: Optional[float] = None
+        self,
+        time: float,
+        new_name: str,
+        tol: float = 0,
+        min_time: Optional[float] = None,
+        max_time: Optional[float] = None,
+        old_name: Optional[str] = None,
     ) -> Tuple[Optional[List[int]], Optional[str], Optional[str]]:
         """Change the name of the annotation.
 
@@ -360,19 +375,21 @@ class Events(UserDict):
             tol (float, optional): Tolerance for matching events. Defaults to 0.
             min_time (Optional[float], optional): _description_. Defaults to None.
             max_time (Optional[float], optional): _description_. Defaults to None.
-
+            old_name (Optional[str]): name of event to move. Defaults to None.
         Returns:
             Tuple[List[int], str, str]: ([start_seconds, stop_seconds], old_name, new_name
             Tuple[None, None, None] if no event near time, or new_name is old_name
         """
-        name = self._get_name_of_nearest(time, min_time, max_time)
+        if old_name is None:
+            name = self._get_name_of_nearest(time, min_time, max_time)
+        else:
+            name = old_name
 
         # nothing to do
         if name is None or name == new_name or self.categories[name] != self.categories[new_name]:
             return None, None, None
 
         index = self._get_index_of_nearest(time, name, tol, min_time, max_time)
-        print(index)
         if index is not None:
             changed_time = self[name][index, :]
             old_name = name

{xarray-behave-0.35.2 → xarray-behave-0.35.4}/src/xarray_behave/gui/app.py

@@ -2,6 +2,7 @@
 
 `python -m xarray_behave.ui datename root`
 """
+
 import os
 import sys
 import logging
@@ -44,7 +45,11 @@ except ImportError:
 try:
     from . import das
 except Exception:
-    logger.warning("Failed to import the das module.\nIgnore if you do not want to use das.\n" "Otherwise follow these instructions to install:\n" "https://janclemenslab.org/das/install.html")
+    logger.warning(
+        "Failed to import the das module.\nIgnore if you do not want to use das.\n"
+        "Otherwise follow these instructions to install:\n"
+        "https://janclemenslab.org/das/install.html"
+    )
 
 sys.setrecursionlimit(10**6)  # increase recursion limit to avoid errors when keeping key pressed for a long time
 package_dir: str = xarray_behave.__path__[0]
@@ -153,7 +158,9 @@ class MainWindow(QtWidgets.QMainWindow):
 
     def save_swaps(self, qt_keycode=None):
         savefilename = self._get_filename_from_ds(suffix="_idswaps.txt")
-        savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(self, "Save swaps to", str(savefilename), filter="txt files (*.txt);;all files (*)")
+        savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(
+            self, "Save swaps to", str(savefilename), filter="txt files (*.txt);;all files (*)"
+        )
         if len(savefilename):
             logger.info(f"   Saving list of swap indices to {savefilename}.")
             os.makedirs(os.path.dirname(savefilename), exist_ok=True)
@@ -162,7 +169,9 @@ class MainWindow(QtWidgets.QMainWindow):
 
     def save_definitions(self, qt_keycode=None):
         savefilename = self._get_filename_from_ds(suffix="_definitions.csv")
-        savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(self, caption="Save definitions to", dir=str(savefilename), filter="CSV files (*_definitions.csv);;all files (*)")
+        savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(
+            self, caption="Save definitions to", dir=str(savefilename), filter="CSV files (*_definitions.csv);;all files (*)"
+        )
         if len(savefilename):
             # get defs from annot and save them to csv
             logger.info(f"   Saving definitions to {savefilename}.")
@@ -402,7 +411,9 @@ class MainWindow(QtWidgets.QMainWindow):
                 self.export_to_h5(savefilename_trunk + ".h5", start_seconds, end_seconds)  # , form_data["scale_audio"])
 
             logger.info(f"   annotations to CSV: {savefilename_trunk + '.csv'}.")
-            self.export_to_csv(savefilename_trunk + "_annotations.csv", start_seconds, end_seconds, which_events, match_to_samples=True)
+            self.export_to_csv(
+                savefilename_trunk + "_annotations.csv", start_seconds, end_seconds, which_events, match_to_samples=True
+            )
             logger.info("Done.")
 
     def das_make(self, qt_keycode=None):
@@ -503,7 +514,9 @@ class MainWindow(QtWidgets.QMainWindow):
             return form_data
 
         def save(arg):
-            savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(self, "Save configuration to", "", filter="yaml files (*.yaml);;all files (*)")
+            savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(
+                self, "Save configuration to", "", filter="yaml files (*.yaml);;all files (*)"
+            )
             if len(savefilename):
                 data = dialog.form.get_form_data()
                 logger.info(f"   Saving form fields to {savefilename}.")
@@ -514,7 +527,9 @@ class MainWindow(QtWidgets.QMainWindow):
         def make_cli(arg):
             script_ext = "cmd" if os.name == "nt" else "sh"
             savefilename = "train." + script_ext
-            savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(self, "Script name", savefilename, filter=f"script (*.{script_ext};;all files (*)")
+            savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(
+                self, "Script name", savefilename, filter=f"script (*.{script_ext};;all files (*)"
+            )
             if len(savefilename):
                 form_data = dialog.form.get_form_data()
                 form_data = _filter_form_data(form_data, is_cli=True)
@@ -696,13 +711,19 @@ class MainWindow(QtWidgets.QMainWindow):
 
                 params = das.utils.load_params(model_path)
                 if audio.shape[0] < params["nb_hist"]:
-                    logger.warning(f"   Aborting. Audio has fewer samples ({audio.shape[0]}) shorter" f"    than network chunk size ({params['nb_hist']})." "    Fix by select longer audio.")
+                    logger.warning(
+                        f"   Aborting. Audio has fewer samples ({audio.shape[0]}) shorter"
+                        f"    than network chunk size ({params['nb_hist']})."
+                        "    Fix by select longer audio."
+                    )
                     return
 
                 # select batch size so that at least 10 batches are run
                 # minimizes loss of annotations from batch size "quantization" errors
                 batch_size = 32
-                nb_batches = lambda batch_size: int(np.floor((audio.shape[0] - ((batch_size - 1) + params["nb_hist"])) / (params["stride"] * (batch_size))))
+                nb_batches = lambda batch_size: int(
+                    np.floor((audio.shape[0] - ((batch_size - 1) + params["nb_hist"])) / (params["stride"] * (batch_size)))
+                )
                 while nb_batches(batch_size) < 10 and batch_size > 1:
                     batch_size -= 1
 
@@ -765,7 +786,11 @@ class MainWindow(QtWidgets.QMainWindow):
                     # segments['sequence'] = [s for s in segments['sequence'] if s is not None]
                     detected_segment_names = np.unique(segments["sequence"])
                     # if these are indices, get corresponding names
-                    if len(detected_segment_names) and type(detected_segment_names[0]) is not str and type(detected_segment_names[0]) is not np.str_:
+                    if (
+                        len(detected_segment_names)
+                        and type(detected_segment_names[0]) is not str
+                        and type(detected_segment_names[0]) is not np.str_
+                    ):
                         detected_segment_names = [segments["names"][ii] for ii in detected_segment_names]
 
                 if len(detected_segment_names) > 0:  # and detected_segment_names[0] is not None:
@@ -781,7 +806,9 @@ class MainWindow(QtWidgets.QMainWindow):
 
                     onsets_seconds = self.ds.sampletime[onsets_samples]
                     offsets_seconds = self.ds.sampletime[offsets_samples]
-                    for name_or_index, onset_seconds, offset_seconds in zip(segments["sequence"], onsets_seconds, offsets_seconds):
+                    for name_or_index, onset_seconds, offset_seconds in zip(
+                        segments["sequence"], onsets_seconds, offsets_seconds
+                    ):
                         if type(name_or_index) is not str and type(detected_segment_names[0]) is not np.str_:
                             segment_name = segments["names"][name_or_index]
                         else:
@@ -830,8 +857,16 @@ class MainWindow(QtWidgets.QMainWindow):
                             except KeyError:
                                 pass
                 except KeyError:
-                    logger.info(f"{filename} no sample rate info in NPZ file." f"Need to save 'samplerate' variable with the audio data. Defaulting to {samplerate}")
-            elif filename.endswith(".h5") or filename.endswith(".hdfs") or filename.endswith(".hdf5") or filename.endswith(".mat"):
+                    logger.info(
+                        f"{filename} no sample rate info in NPZ file."
+                        f"Need to save 'samplerate' variable with the audio data. Defaulting to {samplerate}"
+                    )
+            elif (
+                filename.endswith(".h5")
+                or filename.endswith(".hdfs")
+                or filename.endswith(".hdf5")
+                or filename.endswith(".mat")
+            ):
                 # infer data set (for hdf5) and populate form
                 try:
                     # list all data sets in file and add to list
@@ -935,7 +970,9 @@ class MainWindow(QtWidgets.QMainWindow):
         if not dirname:
             dirname = QtWidgets.QFileDialog.getExistingDirectory(parent=None, caption="Select data directory")
         if dirname:
-            dialog = YamlDialog(yaml_file=package_dir + "/gui/forms/from_dir.yaml", title=f"Dataset from data directory {dirname}")
+            dialog = YamlDialog(
+                yaml_file=package_dir + "/gui/forms/from_dir.yaml", title=f"Dataset from data directory {dirname}"
+            )
 
             # initialize form data with cli args
             dialog.form["pixel_size_mm"] = pixel_size_mm  # and un-disable
@@ -1010,7 +1047,9 @@ class MainWindow(QtWidgets.QMainWindow):
 
                 # add event categories if they are missing in the dataset
                 if "song_events" in ds and "event_categories" not in ds:
-                    event_categories = ["segment" if "sine" in evt or "syllable" in evt else "event" for evt in ds.event_types.values]
+                    event_categories = [
+                        "segment" if "sine" in evt or "syllable" in evt else "event" for evt in ds.event_types.values
+                    ]
                     ds = ds.assign_coords({"event_categories": (("event_types"), event_categories)})
 
                 # add missing song types
@@ -1068,7 +1107,9 @@ class MainWindow(QtWidgets.QMainWindow):
         if not filename:
             filename, _ = QtWidgets.QFileDialog.getOpenFileName(parent=None, caption="Select dataset")
         if filename:
-            dialog = YamlDialog(yaml_file=package_dir + "/gui/forms/from_zarr.yaml", title=f"Load dataset from zarr file {filename}")
+            dialog = YamlDialog(
+                yaml_file=package_dir + "/gui/forms/from_zarr.yaml", title=f"Load dataset from zarr file {filename}"
+            )
 
             # initialize form data with cli args
             if spec_freq_min is not None:
@@ -1106,7 +1147,9 @@ class MainWindow(QtWidgets.QMainWindow):
 
                 # add event categories if they are missing in the dataset
                 if "song_events" in ds and "event_categories" not in ds:
-                    event_categories = ["segment" if "sine" in evt or "syllable" in evt else "event" for evt in ds.event_types.values]
+                    event_categories = [
+                        "segment" if "sine" in evt or "syllable" in evt else "event" for evt in ds.event_types.values
+                    ]
                     ds = ds.assign_coords({"event_categories": (("event_types"), event_categories)})
                 logger.info(ds)
                 vr = None
@@ -1151,11 +1194,15 @@ class MainWindow(QtWidgets.QMainWindow):
 
     def save_dataset(self, qt_keycode=None):
         try:
-            savefilename = Path(self.ds.attrs["root"], self.ds.attrs["dat_path"], self.ds.attrs["datename"], f"{self.ds.attrs['datename']}.zarr")
+            savefilename = Path(
+                self.ds.attrs["root"], self.ds.attrs["dat_path"], self.ds.attrs["datename"], f"{self.ds.attrs['datename']}.zarr"
+            )
         except KeyError:
             savefilename = ""
 
-        savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(self, "Save dataset to", str(savefilename), filter="zarr files (*.zarr);;all files (*)")
+        savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(
+            self, "Save dataset to", str(savefilename), filter="zarr files (*.zarr);;all files (*)"
+        )
 
         if len(savefilename):
             file_exists = os.path.exists(savefilename)
@@ -1310,7 +1357,7 @@ class PSV(MainWindow):
         self.spec_win = 200
         self.show_songevents = True
         self.movable_events = True
-        self.edit_only_current_events = True
+        self.edit_only_current_events = False
         self.show_all_channels = True
         self.select_loudest_channel = False
         self.threshold_mode = False
@@ -1407,10 +1454,16 @@ class PSV(MainWindow):
         self._add_keyed_menuitem(view_video, "Change other fly", self.change_other_fly, "Z")
         self._add_keyed_menuitem(view_video, "Swap flies", self.swap_flies, "X")
         view_video.addSeparator()
-        self._add_keyed_menuitem(view_video, "Move poses", partial(self.toggle, "move_poses"), "B", checkable=True, checked=self.move_poses)
+        self._add_keyed_menuitem(
+            view_video, "Move poses", partial(self.toggle, "move_poses"), "B", checkable=True, checked=self.move_poses
+        )
         view_video.addSeparator()
-        self._add_keyed_menuitem(view_video, "Show fly position", partial(self.toggle, "show_dot"), "O", checkable=True, checked=self.show_dot)
-        self._add_keyed_menuitem(view_video, "Show poses", partial(self.toggle, "show_poses"), "P", checkable=True, checked=self.show_poses)
+        self._add_keyed_menuitem(
+            view_video, "Show fly position", partial(self.toggle, "show_dot"), "O", checkable=True, checked=self.show_dot
+        )
+        self._add_keyed_menuitem(
+            view_video, "Show poses", partial(self.toggle, "show_poses"), "P", checkable=True, checked=self.show_poses
+        )
 
         view_audio = self.bar.addMenu("Audio")
         self._add_keyed_menuitem(view_audio, "Play waveform through speakers", self.play_audio, "E")
@@ -1434,7 +1487,9 @@ class PSV(MainWindow):
         self._add_keyed_menuitem(view_audio, "Select previous channel", self.set_next_channel, "Up")
         self._add_keyed_menuitem(view_audio, "Select next channel", self.set_prev_channel, "Down")
         view_audio.addSeparator()
-        self._add_keyed_menuitem(view_audio, "Show spectrogram", partial(self.toggle, "show_spec"), None, checkable=True, checked=self.show_spec)
+        self._add_keyed_menuitem(
+            view_audio, "Show spectrogram", partial(self.toggle, "show_spec"), None, checkable=True, checked=self.show_spec
+        )
         self._add_keyed_menuitem(view_audio, "Increase frequency resolution", self.inc_freq_res, "R")
         self._add_keyed_menuitem(view_audio, "Increase temporal resolution", self.dec_freq_res, "T")
         view_audio.addSeparator()
@@ -1488,20 +1543,34 @@ class PSV(MainWindow):
         self._add_keyed_menuitem(view_annotations, "Generate proposal by envelope thresholding", self.threshold, "I")
         self._add_keyed_menuitem(view_annotations, "Adjust thresholding mode", self.set_envelope_computation)
         view_annotations.addSeparator()
-        self._add_keyed_menuitem(view_annotations, "Approve proposals for active song type in view", self.approve_active_proposals, "G")
-        self._add_keyed_menuitem(view_annotations, "Approve proposals for all song types in view", self.approve_all_proposals, "H")
+        self._add_keyed_menuitem(
+            view_annotations, "Approve proposals for active song type in view", self.approve_active_proposals, "G"
+        )
+        self._add_keyed_menuitem(
+            view_annotations, "Approve proposals for all song types in view", self.approve_all_proposals, "H"
+        )
 
         view_view = self.bar.addMenu("View")
         self._add_keyed_menuitem(view_view, "Video, waveform, and spectrogram display parameters", self.set_spec_freq)
         view_view.addSeparator()
         # TODO? only show these if tracks and/or video
-        self._add_keyed_menuitem(view_view, "Show spectrogram", partial(self.toggle, "show_spec"), None, checkable=True, checked=self.show_spec)
-        self._add_keyed_menuitem(view_view, "Show waveform", partial(self.toggle, "show_trace"), None, checkable=True, checked=self.show_trace)
-        self._add_keyed_menuitem(view_view, "Show ethogram", partial(self.toggle, "show_annot"), None, checkable=True, checked=self.show_annot)
+        self._add_keyed_menuitem(
+            view_view, "Show spectrogram", partial(self.toggle, "show_spec"), None, checkable=True, checked=self.show_spec
+        )
+        self._add_keyed_menuitem(
+            view_view, "Show waveform", partial(self.toggle, "show_trace"), None, checkable=True, checked=self.show_trace
+        )
+        self._add_keyed_menuitem(
+            view_view, "Show ethogram", partial(self.toggle, "show_annot"), None, checkable=True, checked=self.show_annot
+        )
         if "pose_positions_allo" in self.ds:
-            self._add_keyed_menuitem(view_view, "Show tracks", partial(self.toggle, "show_tracks"), None, checkable=True, checked=self.show_tracks)
+            self._add_keyed_menuitem(
+                view_view, "Show tracks", partial(self.toggle, "show_tracks"), None, checkable=True, checked=self.show_tracks
+            )
         if self.vr is not None:
-            self._add_keyed_menuitem(view_view, "Show movie", partial(self.toggle, "show_movie"), None, checkable=True, checked=self.show_movie)
+            self._add_keyed_menuitem(
+                view_view, "Show movie", partial(self.toggle, "show_movie"), None, checkable=True, checked=self.show_movie
+            )
 
         self.hl = QtWidgets.QHBoxLayout()
 
@@ -1872,7 +1941,9 @@ class PSV(MainWindow):
 
     def delete_current_events(self, qt_keycode):
         if self.current_event_index is not None:
-            deleted_events = self.event_times.delete_range(self.current_event_name, self.time0 / self.fs_song, self.time1 / self.fs_song)
+            deleted_events = self.event_times.delete_range(
+                self.current_event_name, self.time0 / self.fs_song, self.time1 / self.fs_song
+            )
             nb_deleted_events = len(deleted_events)
             if nb_deleted_events:
                 logger.info(f"   Deleted {nb_deleted_events} annotation(s) of type {self.current_event_name}.")
@@ -1894,7 +1965,9 @@ class PSV(MainWindow):
     def threshold(self, qt_keycode):
         if self.STOP and self.current_event_name is not None:
             if self.event_times.categories[self.current_event_name] == "event":
-                indexes = peakutils.indexes(self.envelope, thres=self.slice_view.threshold, min_dist=self.thres_min_dist * self.fs_song, thres_abs=True)
+                indexes = peakutils.indexes(
+                    self.envelope, thres=self.slice_view.threshold, min_dist=self.thres_min_dist * self.fs_song, thres_abs=True
+                )
                 # add events to current song type
                 for t in self.x[indexes]:
                     self.event_times.add_time(self.current_event_name, t)
@@ -2044,7 +2117,9 @@ class PSV(MainWindow):
         dialog.exec_()
 
     def set_envelope_computation(self, qt_keycode):
-        dialog = YamlDialog(yaml_file=package_dir + "/gui/forms/envelope_computation.yaml", title="Set options for envelope computation")
+        dialog = YamlDialog(
+            yaml_file=package_dir + "/gui/forms/envelope_computation.yaml", title="Set options for envelope computation"
+        )
 
         dialog.form["thres_min_dist"] = self.thres_min_dist
         dialog.form["thres_env_std"] = self.thres_env_std
@@ -2122,7 +2197,9 @@ class PSV(MainWindow):
                 i1 = int(self.time1 / self.fs_ratio)
 
                 self.x_tracks = self.ds.time.data[i0:i1]
-                self.y_tracks = self.ds.pose_positions_allo.data[i0:i1, self.focal_fly, self.track_sel_names, self.track_sel_coords]
+                self.y_tracks = self.ds.pose_positions_allo.data[
+                    i0:i1, self.focal_fly, self.track_sel_names, self.track_sel_coords
+                ]
                 self.tracks_view.update_trace()
                 self.tracks_view.show()
             else:
@@ -2169,9 +2246,13 @@ class PSV(MainWindow):
             if self.event_times.categories[event_name] == "segment":
                 for onset, offset in zip(events_in_view[:, 0], events_in_view[:, 1]):
                     if self.show_trace:
-                        self.slice_view.add_segment(onset, offset, event_index, brush=event_brush, pen=event_pen, movable=movable, text=segment_text)
+                        self.slice_view.add_segment(
+                            onset, offset, event_index, brush=event_brush, pen=event_pen, movable=movable, text=segment_text
+                        )
                     if self.show_tracks:
-                        self.tracks_view.add_segment(onset, offset, event_index, brush=event_brush, pen=event_pen, movable=movable, text=segment_text)
+                        self.tracks_view.add_segment(
+                            onset, offset, event_index, brush=event_brush, pen=event_pen, movable=movable, text=segment_text
+                        )
                     if self.show_annot:
                         self.annot_view.add_segment(
                             onset,
@@ -2183,7 +2264,9 @@ class PSV(MainWindow):
                             text=segment_text,
                         )
                     if self.show_spec:
-                        self.spec_view.add_segment(onset, offset, event_index, brush=event_brush, pen=event_pen, movable=movable, text=segment_text)
+                        self.spec_view.add_segment(
+                            onset, offset, event_index, brush=event_brush, pen=event_pen, movable=movable, text=segment_text
+                        )
             elif self.event_times.categories[event_name] == "event":
                 if self.show_trace:
                     self.slice_view.add_event(events_in_view[:, 0], event_index, event_pen, movable=movable, text=segment_text)
@@ -2216,15 +2299,19 @@ class PSV(MainWindow):
 
         new_region = region.getRegion()
         self.event_times.move_time(event_name_to_move, region.bounds, new_region)
-        logger.info(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.")
+        logger.info(
+            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}.")
+        # FIXME for moving annotations in ethogram - fails in pyside6
+        if self.annot_view.mousePoint is not None:
+            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()
 
@@ -2235,19 +2322,20 @@ class PSV(MainWindow):
         event_name_to_move = self.current_event_name
         if self.current_event_index != position.event_index:
             event_name_to_move = self.event_times.names[position.event_index]
-
+        print(position.pos(), position.position)
         new_position = position.pos()[0]
         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}.")
+        # FIXME for moving annotations in ethogram - fails in pyside6
+        if self.annot_view.mousePoint is not None:
+            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_position, new_event_name, old_name=event_name_to_move)
+                if old_name is not None:
+                    logger.info(f"  Changed from {old_name} to {new_name}.")
 
         self.update_xy()
 
@@ -2285,7 +2373,10 @@ class PSV(MainWindow):
                 fly_pos = self.ds.pose_positions_allo.data[self.index_other, :, self.pose_center_index, :]
                 fly_pos = np.array(fly_pos)  # in case this is a dask.array
                 if self.crop:  # transform fly pos to coordinates of the cropped box
-                    box_center = self.ds.pose_positions_allo.data[self.index_other, self.focal_fly, self.pose_center_index] + self.box_size / 2
+                    box_center = (
+                        self.ds.pose_positions_allo.data[self.index_other, self.focal_fly, self.pose_center_index]
+                        + self.box_size / 2
+                    )
                     box_center = np.array(box_center)  # in case this is a dask.array
                     fly_pos = fly_pos - box_center
                 fly_dist = np.sum((fly_pos - np.array([mouseY, mouseX])) ** 2, axis=-1)
@@ -2325,7 +2416,9 @@ class PSV(MainWindow):
                 if self.event_times.categories[self.current_event_name] == "event":
                     logger.info(f"  Changed event at {changed_time[0]:1.4f} from {old_name} to {new_name}.")
                 else:
-                    logger.info(f"  Changed segment at {changed_time[0]:1.4f}:{changed_time[1]:1.4f} from {old_name} to {new_name}.")
+                    logger.info(
+                        f"  Changed segment at {changed_time[0]:1.4f}:{changed_time[1]:1.4f} from {old_name} to {new_name}."
+                    )
                 self.update_xy()
         elif mouseButton == 1:  # add event
             if self.current_event_index is not None:
@@ -2345,12 +2438,16 @@ class PSV(MainWindow):
                             stop_seconds=mouseT,
                             channel=self.current_channel_index,
                         )
-                        logger.info(f"  Added {self.current_event_name} on channel {self.current_channel_index} at t=[{self.sinet0:1.4f}:{mouseT:1.4f}] seconds.")
+                        logger.info(
+                            f"  Added {self.current_event_name} on channel {self.current_channel_index} at t=[{self.sinet0:1.4f}:{mouseT:1.4f}] seconds."
+                        )
                         self.sinet0 = None
                 if self.event_times.categories[self.current_event_name] == "event":
                     self.sinet0 = None
                     self.event_times.add_time(self.current_event_name, start_seconds=mouseT, channel=self.current_channel_index)
-                    logger.info(f"  Added {self.current_event_name} on channel {self.current_channel_index} at t={mouseT:1.4f} seconds.")
+                    logger.info(
+                        f"  Added {self.current_event_name} on channel {self.current_channel_index} at t={mouseT:1.4f} seconds."
+                    )
                 self.update_xy()
             else:
                 self.sinet0 = None

{xarray-behave-0.35.2 → xarray-behave-0.35.4}/src/xarray_behave/gui/das.py

@@ -394,7 +394,9 @@ def make(
     store.attrs["data_splits"] = data_split_dict
     logger.info("Done.")
     # report
-    logger.info(f"  Got {store['train']['x'].shape}, {store['val']['x'].shape}, {store['test']['x'].shape} train/val/test samples.")
+    logger.info(
+        f"  Got {store['train']['x'].shape}, {store['val']['x'].shape}, {store['test']['x'].shape} train/val/test samples."
+    )
     if to_npy_dir:  # save as npy_dir
         logger.info(f"  Saving to {store_folder}.")
         das.npy_dir.save(store_folder, store)
@@ -409,7 +411,9 @@ def make(
         for key in store.keys():
             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
+                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

{xarray-behave-0.35.2 → xarray-behave-0.35.4}/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-0.35.2 → xarray-behave-0.35.4}/src/xarray_behave/gui/views.py

@@ -572,8 +572,6 @@ class AnnotView(pg.PlotWidget):
         # additionally make names of trace and event arrays in ds args?
         super().__init__()
         self.setMouseEnabled(x=False, y=False)
-        # this should be just a link/ref so changes in ds made by the controller will propagate
-        # mabe make Model as thin wrapper around ds that also handles ion and use ref to Modle instance
         self.disableAutoRange()
         self.enableAutoRange(False, False)
         self.setDefaultPadding(0.0)
@@ -655,12 +653,20 @@ class AnnotView(pg.PlotWidget):
         return np.interp(pos, self.xrange, self.m.trange)
 
     def _click(self, event):
-        event.accept()
+        # event.accept()
         pos = event.pos()
         mouseT = self.getPlotItem().getViewBox().mapSceneToView(pos).x()
         self.callback(mouseT, event.button())
 
+    # def mouseMoveEvent(self, ev):
+    #     pos = ev.pos()
+    #     # print(pos)
+    #     if self.sceneBoundingRect().contains(pos):
+    #         self.mousePoint = self.getPlotItem().vb.mapSceneToView(pos)
+    #         print(self.mousePoint)
+
     def mouseMoved(self, pos):
+        # pass
         if self.sceneBoundingRect().contains(pos):
             self.mousePoint = self.getPlotItem().vb.mapSceneToView(pos)
 

{xarray-behave-0.35.2 → xarray-behave-0.35.4}/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-0.35.2 → xarray-behave-0.35.4}/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-0.35.2 → xarray-behave-0.35.4}/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-0.35.2 → xarray-behave-0.35.4}/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
@@ -292,8 +293,12 @@ class Sleap(Poses, io.BaseProvider):
 
         # indices and coordinate logic for sleap tracks. This could be cleaned/simplified later
         nb_flies = tracks.shape[0]
-        thorax_idx = np.argwhere(pose_parts == b"thorax")[0][0]
-        head_idx = np.argwhere(pose_parts == b"head")[0][0]
+        try:
+            thorax_idx = np.argwhere(pose_parts == b"thorax")[0][0]
+            head_idx = np.argwhere(pose_parts == b"head")[0][0]
+        except IndexError:
+            thorax_idx = 0
+            head_idx = 1
         x_idx = 0
         y_idx = 1
 

{xarray-behave-0.35.2 → xarray-behave-0.35.4}/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-0.35.2 → xarray-behave-0.35.4}/src/xarray_behave/metrics.py

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

{xarray-behave-0.35.2 → xarray-behave-0.35.4}/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