Atlas remap (#29)

* save all plots option, new pyqtgraph version changes

* define save path of plots

* save overview plots from GUI

* save improvements, deal with sessions without no track

* Removed video from repo

* catch sessions with no data; attempt to fix c++ wrapper error

* make compatible with latest pyqtgraph

* Update DLC_labeled_video.py

* update requirements

* fix c++ wrapper deleted error

* Atlas3 d features (#23)

* add scatter feature

* option to add region colour values

* option for adding scatter plot and also heatmap over regions on slices

* temporarily add sample data

* double click bugfix

* dual layers with alpha mapping

* colored regions

Co-authored-by: Mayo Faulkner <[email protected]>

* Update DLC_labeled_video.py (#22)

* update requirements, make save plot compatible with offline

* add one setup to travis

* add flatiron pass

* fix import and flake

* Added freeze trigger times and return QC obj

* update extract_files to compute metrics

* add passive plots to GUI

* update experimenter evaluation to probe insertion json in alyx

* passive stuff

* fix bug propagating alignments when starting from 'original'

* add user evaluation tests

* prepare string for dj and alyx

* task_qc_viewer: update doc

* task_qc_viewer: update doc

* only add passive to menu if it exists

* remove flags

* correct path for passive data, filter passive based on units

* remove clusters.metrics.csv if it exists locally

* flake

* catch for nans in spikes.amps

* sync incomplete time series

* brain regions aggregation mappings

* brain regions aggregation mappings (2/2)

Co-authored-by: Mayo Faulkner <[email protected]>
Co-authored-by: Miles Wells <[email protected]>
Co-authored-by: mschart <[email protected]>

Author: 4 people

.flake8

@@ -5,14 +5,7 @@ exclude =
     .git,
     __pycache__,
     __init__.py,
-    data_expoloration_gui/
-    dlc/
+    data_exploration_gui/
     launch_phy/
     histology/
-
-    tutorial_script.py,
-    venv,
-    test_imports.py,
-    build,
-    dist
-    brainbox/
+    qt_matplotlib.py

.travis.yml

@@ -9,6 +9,11 @@ install:
   - pip install git+https://github.com/int-brain-lab/ibllib.git@develop
 
  # command to run tests
+before_script:
+  - echo "exec('from oneibl.one import ONE; ONE(silent=True)')" | python
+  - sed -i 's|null|"'$IBLFLATIRONPASS'"|g' /home/travis/.one_params
+  # command to run tests
+
 script:
   - bash ./run_tests
   - flake8 .

atlaselectrophysiology/ColorBar.py

@@ -17,7 +17,7 @@ def __init__(self, cmap_name, cbin=256, parent=None):
             colors = (cmap(cbins)[np.newaxis, :, :3][0]).tolist()
         else:
             colors = cmap.colors
-        colors = [c + [1.] for c in colors]
+        colors = [(np.array(c) * 255).astype(int).tolist() + [255.] for c in colors]
         positions = np.linspace(0, 1, len(colors))
         self.map = pg.ColorMap(positions, colors)
         self.lut = self.map.getLookupTable()
@@ -30,6 +30,7 @@ def makeColourBar(self, width, height, fig, min=0, max=1, label='', lim=False):
         self.cbar = HorizontalBar(width, height, self.grad)
         ax = fig.getAxis('top')
         ax.setPen('k')
+        ax.setTextPen('k')
         ax.setStyle(stopAxisAtTick=((True, True)))
         # labelStyle = {'font-size': '8pt'}
         ax.setLabel(label)

atlaselectrophysiology/create_overview_plots.py

@@ -0,0 +1,79 @@
+import matplotlib.pyplot as plt
+from pathlib import Path
+import glob
+
+
+def make_overview_plot(folder, sess_info):
+
+    image_folder = folder
+    image_info = sess_info
+
+    def load_image(image_name, ax):
+        with image_name as ifile:
+            image = plt.imread(ifile)
+
+        ax.spines['right'].set_visible(False)
+        ax.spines['top'].set_visible(False)
+        ax.spines['left'].set_visible(False)
+        ax.spines['bottom'].set_visible(False)
+        ax.set_axis_off()
+        ax.set_aspect('equal')
+        ax.imshow(image)
+        return image
+
+    fig = plt.figure(constrained_layout=True, figsize=(18, 9))
+    gs = fig.add_gridspec(3, 18)
+    gs.update(wspace=0.025, hspace=0.05)
+
+    img_row_order = [0, 0, 0, 0, 0, 0, 1, 1, 1]
+    img_column_order = [0, 3, 6, 9, 12, 15, 0, 3, 6]
+    img_idx = [0, 5, 4, 6, 7, 8, 1, 2, 3]
+    img_files = glob.glob(str(image_folder.joinpath(image_info + 'img_*.png')))
+    img_files_sort = [img_files[idx] for idx in img_idx]
+
+    for iF, file in enumerate(img_files_sort):
+        ax = fig.add_subplot(gs[img_row_order[iF], img_column_order[iF]:img_column_order[iF] + 3])
+        load_image(Path(file), ax)
+
+    probe_row_order = [1, 1, 1, 1, 1, 1, 2, 2, 2]
+    probe_column_order = [9, 10, 11, 12, 13, 14, 12, 13, 14]
+    probe_idx = [0, 3, 1, 2, 4, 5, 6]
+    probe_files = glob.glob(str(image_folder.joinpath(image_info + 'probe_*.png')))
+    probe_files_sort = [probe_files[idx] for idx in probe_idx]
+    line_files = glob.glob(str(image_folder.joinpath(image_info + 'line_*.png')))
+
+    for iF, file in enumerate(probe_files_sort + line_files):
+        ax = fig.add_subplot(gs[probe_row_order[iF], probe_column_order[iF]])
+        load_image(Path(file), ax)
+
+    slice_files = glob.glob(str(image_folder.joinpath(image_info + 'slice_*.png')))
+    slice_row_order = [2, 2, 2, 2]
+    slice_idx = [0, 1, 2, 3]
+    slice_column_order = [0, 3, 6, 9]
+    slice_files_sort = [slice_files[idx] for idx in slice_idx]
+
+    for iF, file in enumerate(slice_files_sort):
+        ax = fig.add_subplot(gs[slice_row_order[iF],
+                                slice_column_order[iF]:slice_column_order[iF] + 3])
+        load_image(Path(file), ax)
+
+    slice_files = glob.glob(str(image_folder.joinpath(image_info + 'slice_zoom*.png')))
+    slice_row_order = [2, 2, 2, 2]
+    slice_idx = [0, 1, 2, 3]
+    slice_column_order = [2, 5, 8, 11]
+    slice_files_sort = [slice_files[idx] for idx in slice_idx]
+
+    for iF, file in enumerate(slice_files_sort):
+        ax = fig.add_subplot(gs[slice_row_order[iF], slice_column_order[iF]])
+        load_image(Path(file), ax)
+
+    hist_files = glob.glob(str(image_folder.joinpath(image_info + 'hist*.png')))
+    for iF, file in enumerate(hist_files):
+        ax = fig.add_subplot(gs[1:3, 15:18])
+        load_image(Path(file), ax)
+
+    ax.text(0.5, 0, image_info[:-1], va="center", ha="center", transform=ax.transAxes)
+
+    plt.savefig(image_folder.joinpath(image_info + "overview.png"),
+                bbox_inches='tight', pad_inches=0)
+    plt.show()