xarray-behave 0.35.3__tar.gz → 0.35.5__tar.gz

{xarray-behave-0.35.3 → xarray-behave-0.35.5}/.github/workflows/publish.yaml

@@ -19,11 +19,11 @@ jobs:
     strategy:
       fail-fast: False
       matrix:
-        python-version: [3.9 , '3.10', '3.11']
+        python-version: ['3.10']
         os: [ubuntu-latest, windows-latest, macOS-13, macOS-14]
-        # os: [macOS-13, macOS-14]
-        # python-version: ['3.11']
-        # os: [ubuntu-latest]
+        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-0.35.3 → xarray-behave-0.35.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: xarray-behave
-Version: 0.35.3
+Version: 0.35.5
 Summary: xarray tools for behavioral data.
 Author-email: Jan Clemens <clemensjan@googlemail.com>
 Requires-Python: >3.6

{xarray-behave-0.35.3 → xarray-behave-0.35.5}/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-0.35.3 → xarray-behave-0.35.5}/src/xarray_behave/__init__.py

@@ -1,6 +1,6 @@
 """xarray tools for behavioral data."""
 
-__version__ = "0.35.3"
+__version__ = "0.35.5"
 
 from .xarray_behave import assemble, assemble_metrics, load, save
 import os

{xarray-behave-0.35.3 → xarray-behave-0.35.5}/src/xarray_behave/annot.py

@@ -347,9 +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
 
@@ -359,7 +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.
 
@@ -369,19 +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-0.35.3 → xarray-behave-0.35.5}/src/xarray_behave/gui/app.py

@@ -674,6 +674,10 @@ class MainWindow(QtWidgets.QMainWindow):
             if form_data["segment_minlen"] is None:
                 form_data["segment_minlen"] = 0
 
+            if form_data["filter_song"] == "no":
+                form_data["bandpass_low_freq"] = None
+                form_data["bandpass_up_freq"] = None
+
             if form_data["file"] != "Current file":
                 if form_data["folder"] != " ":
                     file_path = form_data["folder"]
@@ -696,6 +700,9 @@ class MainWindow(QtWidgets.QMainWindow):
                     segment_thres=form_data["event_thres"],
                     segment_fillgap=form_data["segment_fillgap"],
                     segment_minlen=form_data["segment_minlen"],
+                    bandpass_low_freq=form_data["bandpass_low_freq"],
+                    bandpass_up_freq=form_data["bandpass_up_freq"],
+                    resample=form_data["resample"],
                 )
                 return
             elif hasattr(self, "ds") and form_data["file"] == "Current file":
@@ -721,10 +728,10 @@ class MainWindow(QtWidgets.QMainWindow):
                 # 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(
+                nb_batches = 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:
+                while nb_batches < 10 and batch_size > 1:
                     batch_size -= 1
 
                 logger.info("   Running inference on audio.")
@@ -733,10 +740,13 @@ class MainWindow(QtWidgets.QMainWindow):
                 fs_model = params["samplerate_x_Hz"]
                 fs_audio = self.ds.song_raw.attrs["sampling_rate_Hz"]
 
-                if form_data["resample_audio"] and fs_audio and fs_audio != fs_model:
+                if form_data["resample"] and fs_audio and fs_audio != fs_model:
                     logger.info(f"   Resampling. Audio rate is {fs_audio}Hz but model was trained on data with {fs_model}Hz.")
                     audio = das.utils.resample(audio, fs_audio, fs_model)
 
+                import rich
+
+                rich.print(form_data)
                 events, segments, _, _ = das.predict.predict(
                     audio,
                     model_path,
@@ -749,6 +759,10 @@ class MainWindow(QtWidgets.QMainWindow):
                     segment_thres=form_data["event_thres"],
                     segment_fillgap=form_data["segment_fillgap"],
                     segment_minlen=form_data["segment_minlen"],
+                    bandpass_low_freq=form_data["bandpass_low_freq"],
+                    bandpass_up_freq=form_data["bandpass_up_freq"],
+                    resample=form_data["resample"],
+                    fs_audio=fs_audio,
                 )
 
                 # Process detected song
@@ -1357,7 +1371,7 @@ 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
@@ -2303,6 +2317,16 @@ 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."
         )
 
+        # 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()
 
     def on_position_change_finished(self, position):
@@ -2312,11 +2336,21 @@ 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.")
 
+        # 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()
 
     def on_position_dragged(self, fly, pos, offset):

{xarray-behave-0.35.3 → xarray-behave-0.35.5}/src/xarray_behave/gui/forms/das_predict.yaml

@@ -65,11 +65,32 @@ main:
   default: True
   help: Appends '_proposals' to song name. Individual proposals can be corrected and approved.
 
-- name: resample_audio
+- name: resample
   label: Resample audio to rate used for training
   type: bool
   default: True
 
+- name: filter_song
+  label: Bandpass filter audio
+  type: stacked
+  default: "no"
+  options: "no,yes"
+
+  "no":
+
+  "yes":
+  - name: bandpass_low_freq
+    label: Lower cutoff
+    type: double
+    default: 50.0
+    range: 0.0, 1000000.0
+
+  - name: bandpass_up_freq
+    label: Upper cutoff
+    type: double
+    default: 10000.0
+    range: 0.0, 1000000.0
+
 - type: text
   text: '<b>Event detection</b>'
 

{xarray-behave-0.35.3 → xarray-behave-0.35.5}/src/xarray_behave/gui/utils.py

@@ -115,8 +115,7 @@ class FastImageWidget(pg.GraphicsLayoutWidget):
             image_format ([type], optional): [description]. Defaults to QtGui.QImage.Format_RGB888.
             auto_scale (bool, optional): [description]. Defaults to False.
         """
-        qimg = QtGui.QImage(image, image.shape[1], image.shape[0], image_format)
-        # qimg = QtGui.QImage(image.ctypes.data, image.shape[1], image.shape[0], image_format)
+        qimg = QtGui.QImage(image, image.shape[1], image.shape[0], 3 * image.shape[1], image_format)
 
         qpix = QtGui.QPixmap(qimg)
         self.pixmapItem.setPixmap(qpix)

{xarray-behave-0.35.3 → xarray-behave-0.35.5}/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-0.35.3 → xarray-behave-0.35.5}/src/xarray_behave/io/poses.py

@@ -293,8 +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