Merge pull request #126 from int-brain-lab/develop

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int-brain-lab · Sep 3, 2024 · 074eea6 · 074eea6
2 parents a84e54c + fb7f809
commit 074eea6
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Showing 18 changed files with 24 additions and 16 deletions.
diff --git a/atlaselectrophysiology/alignment_with_easyqc.py b/atlaselectrophysiology/alignment_with_easyqc.py
@@ -1,13 +1,13 @@
 from easyqc.gui import viewseis
-from neurodsp import voltage
+from ibldsp import voltage
 import neuropixel
 from viewspikes.data import stream
 from viewspikes.plots import overlay_spikes
 import scipy
 from PyQt5 import QtCore, QtGui
 import numpy as np
 import pyqtgraph as pg
-import qt
+from qt_helpers import qt
 from one.api import ONE
 from iblutil.util import Bunch
 

diff --git a/atlaselectrophysiology/ephys_atlas_gui.py b/atlaselectrophysiology/ephys_atlas_gui.py
@@ -20,7 +20,7 @@
 from ephysfeatures.features_across_region import RegionFeatureWindow
 from atlaselectrophysiology.create_overview_plots import make_overview_plot
 from pathlib import Path
-import qt
+from qt_helpers import qt
 import matplotlib.pyplot as mpl  # noqa  # This is needed to make qt show properly :/
 
 
@@ -2149,6 +2149,14 @@ def viewer(probe_id, one=None, histology=False, spike_collection=None, title=Non
     return av
 
 
+def launch_offline():
+
+    app_off = QtWidgets.QApplication([])
+    mainapp_off = MainWindow(offline=True)
+    mainapp_off.show()
+    app_off.exec_()
+
+
 if __name__ == '__main__':
 
     import argparse

diff --git a/atlaselectrophysiology/extract_files.py b/atlaselectrophysiology/extract_files.py
@@ -4,7 +4,7 @@
 from tqdm import tqdm
 import spikeglx
 import numpy as np
-from neurodsp import fourier, utils
+from ibldsp import fourier, utils
 from scipy import signal
 import one.alf.io as alfio
 import ibllib.ephys.ephysqc as ephysqc

diff --git a/atlaselectrophysiology/plot_data.py b/atlaselectrophysiology/plot_data.py
@@ -4,7 +4,7 @@
 from brainbox.io.spikeglx import Streamer
 from brainbox.population.decode import xcorr
 from brainbox.task import passive
-from neurodsp import voltage
+from ibldsp import voltage
 import neuropixel
 import scipy
 from PyQt5 import QtGui

diff --git a/atlasview/atlasview.py b/atlasview/atlasview.py
@@ -21,7 +21,7 @@
 import matplotlib
 
 from iblatlas.atlas import AllenAtlas
-import qt
+from qt_helpers import qt
 
 
 class TopView(QtWidgets.QMainWindow):

diff --git a/data_exploration_gui/data_explore_gui.py b/data_exploration_gui/data_explore_gui.py
@@ -15,7 +15,7 @@
 import data_exploration_gui.data_model as dat
 from data_exploration_gui import utils
 
-import qt
+from qt_helpers import qt
 import matplotlib.pyplot as mpl  # noqa  # This is needed to make qt show properly :/
 from one.api import ONE
 

diff --git a/data_exploration_gui/gui_main.py b/data_exploration_gui/gui_main.py
@@ -12,7 +12,7 @@
 from pathlib import Path
 import numpy as np
 
-import qt
+from qt_helpers import qt
 import matplotlib.pyplot as mpl  # noqa  # This is needed to make qt show properly :/
 
 

diff --git a/dlc/DLC_labeled_video.py b/dlc/DLC_labeled_video.py
@@ -7,7 +7,7 @@
 import pandas as pd
 # conda install -c conda-forge pyarrow
 import os
-from neurodsp.smooth import smooth_interpolate_savgol
+from ibldsp.smooth import smooth_interpolate_savgol
 from brainbox.io.one import SessionLoader
 from copy import deepcopy
 

diff --git a/ephysfeatures/__init__.py b/ephysfeatures/__init__.py
diff --git a/histology/atlas_mpl.py b/histology/atlas_mpl.py
@@ -3,8 +3,8 @@
 import numpy as np
 from PyQt5 import QtCore, QtWidgets, uic
 
-from iblapps import qt
-from iblapps.qt_matplotlib import BaseMplCanvas
+from qt_helpers import qt
+from qt_helpers.qt_matplotlib import BaseMplCanvas
 import iblatlas.atlas as atlas
 
 # Make sure that we are using QT5

diff --git a/needles2/probe_model.py b/needles2/probe_model.py
@@ -12,7 +12,7 @@
 from iblatlas import atlas
 from neuropixel import TIP_SIZE_UM, trace_header
 from ibllib.pipes.ephys_alignment import EphysAlignment
-from neurodsp.utils import fcn_cosine
+from ibldsp.utils import fcn_cosine
 
 PROV_2_VAL = {
     'Resolved': 90,

diff --git a/needles2/run_needles2.py b/needles2/run_needles2.py
@@ -11,7 +11,7 @@
 
 from iblatlas.atlas import AllenAtlas, Insertion
 
-import qt
+from qt_helpers import qt
 
 from one.api import ONE
 from needles2.probe_model import ProbeModel

diff --git a/needles2/spike_features.py b/needles2/spike_features.py
@@ -1,7 +1,7 @@
 from PyQt5 import QtWidgets, QtGui, QtCore
 import pyqtgraph as pg
 import pyqtgraph.exporters
-import qt
+from qt_helpers import qt
 import atlaselectrophysiology.ColorBar as cb
 
 from dataclasses import dataclass, field

diff --git a/qt_helpers/__init__.py b/qt_helpers/__init__.py
diff --git a/qt.py → qt_helpers/qt.py b/qt.py → qt_helpers/qt.py
diff --git a/qt_matplotlib.py → qt_helpers/qt_matplotlib.py b/qt_matplotlib.py → qt_helpers/qt_matplotlib.py
diff --git a/setup.py b/setup.py
@@ -12,7 +12,7 @@
     entry_points={
         'console_scripts': [
             'atlas=atlasview.atlasview:main',
-            'align=atlaselectrophysiology.ephys_atlas_gui:main',
+            'ephys-align=atlaselectrophysiology.ephys_atlas_gui:launch_offline',
         ]
     },
 )
diff --git a/viewspikes/load_ma_data.py b/viewspikes/load_ma_data.py
@@ -1,7 +1,7 @@
 from one.api import ONE
 import one.alf.io as alfio
 from iblutil.util import Bunch
-import qt
+from qt_helpers import qt
 import numpy as np
 import pyqtgraph as pg