Merge pull request #100 from int-brain-lab/atlas_imports

Atlas imports

atlaselectrophysiology/compare_alignments.py

@@ -4,7 +4,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
 import matplotlib
-import ibllib.atlas as atlas
+import iblatlas.atlas as atlas
 from pathlib import Path
 # Instantiate brain atlas and one
 brain_atlas = atlas.AllenAtlas(25)

atlaselectrophysiology/get_scale_factor.py

@@ -12,7 +12,7 @@
 import pandas as pd
 import matplotlib.pyplot as plt
 import seaborn as sns
-import ibllib.atlas as atlas
+import iblatlas.atlas as atlas
 
 
 # Instantiate brain atlas and one

atlaselectrophysiology/load_data.py

@@ -3,7 +3,7 @@
 from datetime import datetime
 import ibllib.pipes.histology as histology
 from neuropixel import trace_header
-import ibllib.atlas as atlas
+import iblatlas.atlas as atlas
 from ibllib.qc.alignment_qc import AlignmentQC
 from iblutil.numerical import ismember
 from iblutil.util import Bunch

atlaselectrophysiology/load_data_local.py

@@ -1,7 +1,7 @@
 import logging
 import numpy as np
 from datetime import datetime
-import ibllib.atlas as atlas
+import iblatlas.atlas as atlas
 from pathlib import Path
 import one.alf.io as alfio
 from one import alf

atlasview/atlasview.py

@@ -2,7 +2,7 @@
 TopView is the main Widget with the related ControllerTopView Class
 There are several SliceView windows (sagittal, coronal, possibly tilted etc...) that each have
 a SliceController object
-The underlying data model object is an ibllib.atlas.AllenAtlas object
+The underlying data model object is an iblatlas.atlas.AllenAtlas object
 
     TopView(QMainWindow)
     ControllerTopView(PgImageController)
@@ -20,7 +20,7 @@
 import pyqtgraph as pg
 import matplotlib
 
-from ibllib.atlas import AllenAtlas
+from iblatlas.atlas import AllenAtlas
 import qt
 
 
@@ -85,7 +85,7 @@ def add_image_layer(self, **kwargs):
         """
         :param pg_kwargs: pyqtgraph setImage arguments: {'levels': None, 'lut': None,
         'opacity': 1.0}
-        :param slice_kwargs: ibllib.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
+        :param slice_kwargs: iblatlas.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
         :return:
         """
         self.ctrl.fig_sagittal.add_image_layer(**kwargs)
@@ -160,7 +160,7 @@ def add_image_layer(self, **kwargs):
         """
         :param pg_kwargs: pyqtgraph setImage arguments: {'levels': None, 'lut': None,
         'opacity': 1.0}
-        :param slice_kwargs: ibllib.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
+        :param slice_kwargs: iblatlas.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
         :return:
         """
         il = ImageLayer(**kwargs)
@@ -354,7 +354,7 @@ class ImageLayer:
     Class for keeping track of image layers.
     :param image_item
     :param pg_kwargs: pyqtgraph setImage arguments: {'levels': None, 'lut': None, 'opacity': 1.0}
-    :param slice_kwargs: ibllib.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
+    :param slice_kwargs: iblatlas.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
     :param
     """
     image_item: pg.ImageItem = field(default_factory=pg.ImageItem)

ephysfeatures/features_across_region.py

@@ -7,7 +7,7 @@
 import pandas as pd
 import numpy as np
 
-from ibllib.atlas import AllenAtlas
+from iblatlas.atlas import AllenAtlas
 import atlaselectrophysiology.ColorBar as cb
 from ibllib.pipes.ephys_alignment import EphysAlignment
 from atlaselectrophysiology.AdaptedAxisItem import replace_axis

histology/atlas_mpl.py

@@ -5,7 +5,7 @@
 
 from iblapps import qt
 from iblapps.qt_matplotlib import BaseMplCanvas
-import ibllib.atlas as atlas
+import iblatlas.atlas as atlas
 
 # Make sure that we are using QT5
 matplotlib.use('Qt5Agg')

launch_phy/phy_launcher.py

@@ -23,7 +23,7 @@ def launch_phy(probe_name=None, eid=None, pid=None, subj=None, date=None, sess_n
     # -------------------- #
 
     from one.api import ONE
-    from ibllib.atlas import AllenAtlas
+    from iblatlas.atlas import AllenAtlas
     from brainbox.io.one import SpikeSortingLoader
     from ibllib.io import spikeglx
     one = ONE()

needles2/probe_model.py

@@ -8,7 +8,8 @@
 from iblutil.numerical import ismember
 
 from ibllib.pipes import histology
-from ibllib.atlas import AllenAtlas, atlas
+from iblatlas.atlas import AllenAtlas
+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

needles2/run_needles2.py

@@ -9,7 +9,7 @@
 import pyqtgraph as pg
 import matplotlib
 
-from ibllib.atlas import AllenAtlas, Insertion
+from iblatlas.atlas import AllenAtlas, Insertion
 
 import qt
 
@@ -1219,7 +1219,7 @@ def add_image_layer(self, idx=None, **kwargs):
         :param name: name of the image item to keep track of layers
         :param pg_kwargs: pyqtgraph setImage arguments: {'levels': None, 'lut': None,
         'opacity': 1.0}
-        :param slice_kwargs: ibllib.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
+        :param slice_kwargs: iblatlas.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
         :return:
         """
         il = ImageLayer(**kwargs)
@@ -1342,7 +1342,7 @@ def add_scatter(self, idx=None, **kwargs):
         :param name: name of the image item to keep track of layers
         :param pg_kwargs: pyqtgraph setImage arguments: {'levels': None, 'lut': None,
         'opacity': 1.0}
-        :param slice_kwargs: ibllib.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
+        :param slice_kwargs: iblatlas.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
         :return:
         """
         sc = ScatterLayer(**kwargs)
@@ -1429,7 +1429,7 @@ class ImageLayer:
     Class for keeping track of image layers.
     :param image_item
     :param pg_kwargs: pyqtgraph setImage arguments: {'levels': None, 'lut': None, 'opacity': 1.0}
-    :param slice_kwargs: ibllib.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
+    :param slice_kwargs: iblatlas.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
     :param
     """
     name: str = field(default='base')

needles2/spike_features.py

@@ -458,7 +458,7 @@ class SpikeSortFigures:
     Class for keeping track of image layers.
     :param image_item
     :param pg_kwargs: pyqtgraph setImage arguments: {'levels': None, 'lut': None, 'opacity': 1.0}
-    :param slice_kwargs: ibllib.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
+    :param slice_kwargs: iblatlas.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
     :param
     """
     name: str = field(default='base')
@@ -473,7 +473,7 @@ class SpikeSortRawData:
     Class for keeping track of image layers.
     :param image_item
     :param pg_kwargs: pyqtgraph setImage arguments: {'levels': None, 'lut': None, 'opacity': 1.0}
-    :param slice_kwargs: ibllib.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
+    :param slice_kwargs: iblatlas.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
     :param
     """
     name: str = field(default='base')
@@ -488,7 +488,7 @@ class SpikeSortPlotData:
     Class for keeping track of image layers.
     :param image_item
     :param pg_kwargs: pyqtgraph setImage arguments: {'levels': None, 'lut': None, 'opacity': 1.0}
-    :param slice_kwargs: ibllib.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
+    :param slice_kwargs: iblatlas.atlas.slice arguments: {'volume': 'image', 'mode': 'clip'}
     :param
     """
     name: str = field(default='base')

tests/test_alignment_qc_gui.py

@@ -6,7 +6,7 @@
 import numpy as np
 
 from one.api import ONE
-from ibllib.atlas import AllenAtlas
+from iblatlas.atlas import AllenAtlas
 from atlaselectrophysiology.load_data import LoadData
 from ibllib.pipes.ephys_alignment import EphysAlignment
 from ibllib.pipes.misc import create_alyx_probe_insertions

viewspikes/examples_local.py

@@ -89,7 +89,7 @@
  'clusters.channels',
  'clusters.mlapdv']
 
-from ibllib.atlas import atlas
+from iblatlas import atlas
 from ibllib.pipes import histology
 from ibllib.ephys import neuropixel
 

viewspikes/plots.py

@@ -4,7 +4,7 @@
 import scipy.signal
 import pyqtgraph as pg
 
-import ibllib.atlas as atlas
+import iblatlas.atlas as atlas
 from neuropixel import SITES_COORDINATES
 from ibllib.pipes.ephys_alignment import EphysAlignment
 from ibllib.plots import wiggle, color_cycle