xarray-behave 0.34.0__tar.gz → 0.34.2__tar.gz

{xarray-behave-0.34.0 → xarray-behave-0.34.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: xarray-behave
-Version: 0.34.0
+Version: 0.34.2
 Summary: xarray tools for behavioral data.
 Author-email: Jan Clemens <clemensjan@googlemail.com>
 Requires-Python: >3.6

{xarray-behave-0.34.0 → xarray-behave-0.34.2}/conda/xarray-behave/build.sh

@@ -4,6 +4,8 @@ export PIP_NO_INDEX=False
 export PIP_NO_DEPENDENCIES=False
 export PIP_IGNORE_INSTALLED=False
 
-$PYTHON -m pip install simpleaudio -vv --no-dependencies
+if [[ "$OSTYPE" == "darwin"* ]]; then
+  $PYTHON -m pip install simpleaudio -vv --no-dependencies
+fi
 $PYTHON -m pip install pkgutil_resolve_name -vv --no-dependencies
 $PYTHON -m pip install xarray-behave[gui] -vv --no-dependencies

{xarray-behave-0.34.0 → xarray-behave-0.34.2}/conda/xarray-behave/meta.yaml

@@ -16,7 +16,6 @@ requirements:
   host:
     - python {{ python }}
     - pip
-    - numpy>1.20  #<1.24
   run:
     - python {{ python }}
     - defopt=6.3
@@ -32,6 +31,7 @@ requirements:
     - scikit-learn
     - zarr
     - numba>=0.56
+    # - anaconda::_openmp_mutex>=5.1  # [linux and py>=3.11]
     - xarray
     - dask
     - pyside2 # [not win]

{xarray-behave-0.34.0 → xarray-behave-0.34.2}/src/xarray_behave/__init__.py

@@ -1,5 +1,5 @@
 """xarray tools for behavioral data."""
-__version__ = "0.34.0"
+__version__ = "0.34.2"
 
 from .xarray_behave import assemble, assemble_metrics, load, save
 import os

{xarray-behave-0.34.0 → xarray-behave-0.34.2}/src/xarray_behave/event_utils.py

@@ -16,7 +16,7 @@ def detect_events(ds):
         dict: with event times or segment on/offsets.
     """
     event_times = dict()
-    ds.song_events.data = ds.song_events.data.astype(np.float)  # make sure this is non-bool so diff works
+    ds.song_events.data = ds.song_events.data.astype(float)  # make sure this is non-bool so diff works
     event_names = ds.song_events.event_types.data
     event_categories = ds.song_events.event_categories.data
     logger.info("Extracting event times from song_events:")

{xarray-behave-0.34.0 → xarray-behave-0.34.2}/src/xarray_behave/gui/app.py

@@ -2000,7 +2000,7 @@ class PSV(MainWindow):
                     logger.info(f"   Removed {old_len - new_len} duplicates in {self.current_event_name}.")
             if self.event_times.categories[self.current_event_name] == "segment":
                 # get pos and neg crossings
-                x = np.diff((self.envelope > self.slice_view.threshold).astype(np.float))
+                x = np.diff((self.envelope > self.slice_view.threshold).astype(float))
                 onsets = np.where(x == 1)[0]
                 offsets = np.where(x == -1)[0]
                 # remove incomplete segments at bounds
@@ -2019,7 +2019,7 @@ class PSV(MainWindow):
         std = self.thres_env_std * self.fs_song
         win = scipy.signal.windows.gaussian(int(std * 6), std)
         win /= np.sum(win)
-        env = np.sqrt(np.convolve(self.y.astype(np.float) ** 2, win, mode="same"))
+        env = np.sqrt(np.convolve(self.y.astype(float) ** 2, win, mode="same"))
         return env
 
     def set_prev_channel(self, qt_keycode):

{xarray-behave-0.34.0 → xarray-behave-0.34.2}/src/xarray_behave/gui/forms/das_train.yaml

@@ -158,6 +158,30 @@ main:
   help: Reduce learning rate if performance does not improve after patience epochs.
 
 
+- name: morph
+  label: Postprocessing with trainable morphological kernels
+  type: stacked
+  default: "No"
+  options: "No,Yes"
+
+  "No":
+
+  "Yes":
+  - type: text
+    text: 'Clean up predictions using trainable kernels for opening and closing operations.'
+
+  - name: morph_nb_kernels
+    label:  Number of morphological kernels
+    type: int
+    default: 1
+    range: 0, 100
+  - name: morph_kernel_duration
+    label: Duration of morphological kernels (samples)
+    type: int
+    default: 32
+    range: 1,1000
+
+
 - name: postopt
   label: Optimize postprocessing
   type: stacked

{xarray-behave-0.34.0 → xarray-behave-0.34.2}/src/xarray_behave/gui/views.py

@@ -256,7 +256,7 @@ class TraceView(pg.PlotWidget):
         # plot active channel
         x = self.m.x[:: self.m.step]
         item = pg.PlotCurveItem(
-            x=x, y=np.array(self.m.y[:: self.m.step], dtype=np.float), pen=pg.mkPen(color=[220, 220, 220], width=1)
+            x=x, y=np.array(self.m.y[:: self.m.step], dtype=float), pen=pg.mkPen(color=[220, 220, 220], width=1)
         )
         self.addItem(item)
         # self.autoRange(padding=0)

{xarray-behave-0.34.0 → xarray-behave-0.34.2}/src/xarray_behave/io/annotations.py

@@ -12,8 +12,8 @@ logger = logging.getLogger(__name__)
 
 
 def fill_gaps(sine_pred, gap_dur=100):
-    onsets = np.where(np.diff(sine_pred.astype(np.int)) == 1)[0]
-    offsets = np.where(np.diff(sine_pred.astype(np.int)) == -1)[0]
+    onsets = np.where(np.diff(sine_pred.astype(int)) == 1)[0]
+    offsets = np.where(np.diff(sine_pred.astype(int)) == -1)[0]
     if len(onsets) and len(offsets):
         onsets = onsets[onsets < offsets[-1]]
         offsets = offsets[offsets > onsets[0]]
@@ -26,8 +26,8 @@ def fill_gaps(sine_pred, gap_dur=100):
 
 def remove_short(sine_pred, min_len=100):
     # remove too short sine songs
-    onsets = np.where(np.diff(sine_pred.astype(np.int)) == 1)[0]
-    offsets = np.where(np.diff(sine_pred.astype(np.int)) == -1)[0]
+    onsets = np.where(np.diff(sine_pred.astype(int)) == 1)[0]
+    offsets = np.where(np.diff(sine_pred.astype(int)) == -1)[0]
     if len(onsets) and len(offsets):
         onsets = onsets[onsets < offsets[-1]]
         offsets = offsets[offsets > onsets[0]]
@@ -73,8 +73,8 @@ class DAS(io.BaseProvider):
                     segment_labels = remove_short(segment_labels, min_len=0.02 * res["samplerate_Hz"])
 
                 # detect on and offset from binary labels
-                segment_onset_idx = np.where(np.diff(segment_labels.astype(np.float), prepend=0) == 1)[0].astype(np.float)
-                segment_offset_idx = np.where(np.diff(segment_labels.astype(np.float), append=0) == -1)[0].astype(np.float)
+                segment_onset_idx = np.where(np.diff(segment_labels.astype(float), prepend=0) == 1)[0].astype(float)
+                segment_offset_idx = np.where(np.diff(segment_labels.astype(float), append=0) == -1)[0].astype(float)
 
                 res["segment_onsets_seconds"] = np.append(
                     res["segment_onsets_seconds"], segment_onset_idx / res["samplerate_Hz"]

{xarray-behave-0.34.0 → xarray-behave-0.34.2}/src/xarray_behave/io/poses.py

@@ -157,7 +157,7 @@ class Leap(Poses, io.BaseProvider):
 
         with h5py.File(filename, "r") as f:
             box_offset = f["box_centers"][:]
-            box_angle = f["fixed_angles"][:].astype(np.float64)
+            box_angle = f["fixed_angles"][:].astype(float)
             box_size = (f["box_size"].attrs["i0"], f["box_size"].attrs["i1"])
             poses = f["positions"][:]
             nb_flies = int(np.max(f["fly_id"]) + 1)
@@ -181,7 +181,7 @@ class Leap(Poses, io.BaseProvider):
         box_offset = box_offset[first_pose_index:last_pose_index, ...]
         box_angle = box_angle[first_pose_index:last_pose_index, ...]
         poses = poses[first_pose_index:last_pose_index, ...]
-        poses = poses.astype(np.float64)
+        poses = poses.astype(float)
 
         # transform poses back to frame coordinates
         origin = [b / 2 for b in box_size]