xarray-behave 0.35.0__tar.gz → 0.35.2__tar.gz

{xarray-behave-0.35.0 → xarray-behave-0.35.2}/.github/workflows/publish.yaml

@@ -19,15 +19,16 @@ jobs:
     strategy:
       fail-fast: False
       matrix:
-        python-version: [3.9 , '3.10', '3.11']
-        os: [ubuntu-latest, windows-latest, macOS-13, macOS-14]
+        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
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Setup miniconda # https://github.com/marketplace/actions/setup-miniconda
       uses: conda-incubator/setup-miniconda@v3
       with:

{xarray-behave-0.35.0 → xarray-behave-0.35.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: xarray-behave
-Version: 0.35.0
+Version: 0.35.2
 Summary: xarray tools for behavioral data.
 Author-email: Jan Clemens <clemensjan@googlemail.com>
 Requires-Python: >3.6

{xarray-behave-0.35.0 → xarray-behave-0.35.2}/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-0.35.0 → xarray-behave-0.35.2}/src/xarray_behave/__init__.py

@@ -1,5 +1,5 @@
 """xarray tools for behavioral data."""
-__version__ = "0.35.0"
+__version__ = "0.35.2"
 
 from .xarray_behave import assemble, assemble_metrics, load, save
 import os

{xarray-behave-0.35.0 → xarray-behave-0.35.2}/src/xarray_behave/annot.py

@@ -132,19 +132,20 @@ 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
 
@@ -165,9 +166,7 @@ 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
 
@@ -196,16 +195,12 @@ 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")
@@ -315,9 +310,7 @@ 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)

{xarray-behave-0.35.0 → xarray-behave-0.35.2}/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-0.35.0 → xarray-behave-0.35.2}/src/xarray_behave/gui/app.py

@@ -44,11 +44,7 @@ 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]
@@ -157,9 +153,7 @@ 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)
@@ -168,9 +162,7 @@ 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}.")
@@ -410,9 +402,7 @@ 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):
@@ -513,9 +503,7 @@ 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}.")
@@ -526,9 +514,7 @@ 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)
@@ -710,19 +696,13 @@ 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
 
@@ -785,11 +765,7 @@ 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:
@@ -805,9 +781,7 @@ 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:
@@ -856,16 +830,8 @@ 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
@@ -969,9 +935,7 @@ 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
@@ -1046,9 +1010,7 @@ 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
@@ -1106,9 +1068,7 @@ 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:
@@ -1146,9 +1106,7 @@ 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
@@ -1193,15 +1151,11 @@ 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)
@@ -1453,16 +1407,10 @@ 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")
@@ -1486,9 +1434,7 @@ 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()
@@ -1542,34 +1488,20 @@ 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()
 
@@ -1940,9 +1872,7 @@ 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}.")
@@ -1964,9 +1894,7 @@ 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)
@@ -2116,9 +2044,7 @@ 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
@@ -2196,9 +2122,7 @@ 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:
@@ -2245,13 +2169,9 @@ 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,
@@ -2263,9 +2183,7 @@ 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)
@@ -2298,9 +2216,7 @@ 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:
@@ -2369,10 +2285,7 @@ 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)
@@ -2412,9 +2325,7 @@ 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:
@@ -2434,16 +2345,12 @@ 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
@@ -2807,3 +2714,7 @@ def cli():
         logger.getLogger().setLevel(logging.INFO)
 
     defopt.run(main, show_defaults=False)
+
+
+if __name__ == "__main__":
+    main_das()

{xarray-behave-0.35.0 → xarray-behave-0.35.2}/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
@@ -393,9 +394,7 @@ 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)
@@ -408,8 +407,12 @@ 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-0.35.0 → xarray-behave-0.35.2}/src/xarray_behave/gui/views.py

@@ -584,7 +584,7 @@ class AnnotView(pg.PlotWidget):
         self.scene().sigMouseMoved.connect(self.mouseMoved)
 
         self.annotation_items = []
-        self.getAxis("left").setStyle(tickFont=self.m.font_condensed)
+        # self.getAxis("left").setStyle(tickFont=self.m.font_condensed)
         self.getAxis("left").setWidth(50)
 
         self.mousePoint = None