diff --git a/atlaselectrophysiology/compare_alignments.py b/atlaselectrophysiology/compare_alignments.py index d09de30..e4e4298 100644 --- a/atlaselectrophysiology/compare_alignments.py +++ b/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) diff --git a/atlaselectrophysiology/get_scale_factor.py b/atlaselectrophysiology/get_scale_factor.py index a2ceb73..90fa288 100644 --- a/atlaselectrophysiology/get_scale_factor.py +++ b/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 diff --git a/atlaselectrophysiology/load_data.py b/atlaselectrophysiology/load_data.py index c8906c1..26c5a71 100644 --- a/atlaselectrophysiology/load_data.py +++ b/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 diff --git a/atlaselectrophysiology/load_data_local.py b/atlaselectrophysiology/load_data_local.py index 78c5a6a..24e29a3 100644 --- a/atlaselectrophysiology/load_data_local.py +++ b/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 diff --git a/atlasview/atlasview.py b/atlasview/atlasview.py index efb8d18..fe30360 100644 --- a/atlasview/atlasview.py +++ b/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) diff --git a/ephysfeatures/features_across_region.py b/ephysfeatures/features_across_region.py index 7111f84..929e9a0 100644 --- a/ephysfeatures/features_across_region.py +++ b/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 diff --git a/histology/atlas_mpl.py b/histology/atlas_mpl.py index f51ec01..086f2bd 100644 --- a/histology/atlas_mpl.py +++ b/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') diff --git a/launch_phy/phy_launcher.py b/launch_phy/phy_launcher.py index d0925c0..6796db2 100644 --- a/launch_phy/phy_launcher.py +++ b/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() diff --git a/needles2/probe_model.py b/needles2/probe_model.py index da631be..feeec00 100644 --- a/needles2/probe_model.py +++ b/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 diff --git a/needles2/run_needles2.py b/needles2/run_needles2.py index f7ba1d5..2f4337f 100644 --- a/needles2/run_needles2.py +++ b/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') diff --git a/needles2/spike_features.py b/needles2/spike_features.py index 6c40826..a769168 100644 --- a/needles2/spike_features.py +++ b/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') diff --git a/tests/test_alignment_qc_gui.py b/tests/test_alignment_qc_gui.py index 7977bd5..e61e1bb 100644 --- a/tests/test_alignment_qc_gui.py +++ b/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 diff --git a/viewspikes/examples_local.py b/viewspikes/examples_local.py index dfe3815..bd2ab40 100644 --- a/viewspikes/examples_local.py +++ b/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 diff --git a/viewspikes/plots.py b/viewspikes/plots.py index 611e92d..2601d34 100644 --- a/viewspikes/plots.py +++ b/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