Fix data loading & lint (#53)

* fix plugin name * Update pre-commit * update plugin names * fix pandas warning * remove deprecated napari code * Bump version: 0.2.14 → 0.2.15-rc0 * remove deprecated napari code * Bump version: 0.2.15-rc0 → 0.2.16-rc0 * Bump version: 0.2.16-rc0 → 0.2.16
brainglobe · Jun 15, 2022 · 1390077 · 1390077
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,12 +1,30 @@
 repos:
--   repo: https://github.com/python/black
-    rev: 20.8b1
-    hooks:
-    - id: black
-      pass_filenames: true
--   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.7.9
-    hooks:
-    - id: flake8
-      pass_filenames: true
-#      exclude: __init__.py
+    - repo: https://github.com/pycqa/isort
+      rev: 5.10.1
+      hooks:
+          - id: isort
+            types: [text]
+            types_or: [python, cython]
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.1.0
+      hooks:
+          - id: check-docstring-first
+          - id: check-executables-have-shebangs
+          - id: check-merge-conflict
+          - id: check-toml
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: requirements-txt-fixer
+          - id: trailing-whitespace
+            # bump2version produces whitespace in setup.cfg, so exclude to
+            # not inferfere with versioning
+            exclude: setup.cfg
+    - repo: https://gitlab.com/pycqa/flake8
+      rev: 3.9.2
+      hooks:
+          - id: flake8
+    - repo: https://github.com/psf/black
+      rev: 22.3.0
+      hooks:
+          - id: black
diff --git a/README.md b/README.md
@@ -17,9 +17,9 @@ Segmentation of 1/2/3D brain structures in a common anatomical space
 
 ## Installation
 
-brainreg-segment comes bundled with [`brainreg`](https://github.com/brainglobe/brainreg), so see the [brainreg installation instructions](https://docs.brainglobe.info/brainreg/installation). 
+brainreg-segment comes bundled with [`brainreg`](https://github.com/brainglobe/brainreg), so see the [brainreg installation instructions](https://docs.brainglobe.info/brainreg/installation).
 
-brainreg-segment can be installed on it's own (`pip install brainreg-segment`), but you will need to register your data with brainreg first. 
+brainreg-segment can be installed on it's own (`pip install brainreg-segment`), but you will need to register your data with brainreg first.
 
 ## Usage
 
@@ -40,4 +40,3 @@ If you find brainreg-segment useful, and use it in your research, please let us
 The BrainGlobe project is generously supported by the Sainsbury Wellcome Centre and the Institute of Neuroscience, Technical University of Munich, with funding from Wellcome, the Gatsby Charitable Foundation and the Munich Cluster for Systems Neurology - Synergy.
 
 <img src='https://brainglobe.info/images/logos_combined.png' width="550">
-
diff --git a/brainreg_segment/__init__.py b/brainreg_segment/__init__.py
@@ -1,3 +1,3 @@
 __author__ = "Adam Tyson"
-__version__ = "0.2.14"
+__version__ = "0.2.16"
 from . import *
diff --git a/brainreg_segment/atlas/utils.py b/brainreg_segment/atlas/utils.py
@@ -1,5 +1,6 @@
 import re
-from bg_atlasapi.list_atlases import utils, descriptors
+
+from bg_atlasapi.list_atlases import descriptors, utils
 
 
 def lateralise_atlas_image(

diff --git a/brainreg_segment/layout/gui_elements.py b/brainreg_segment/layout/gui_elements.py
@@ -2,12 +2,12 @@
 # from napari.resources import build_icons # Contains .SVGPATH to all icons for napari
 
 from qtpy.QtWidgets import (
-    QDoubleSpinBox,
-    QPushButton,
     QCheckBox,
+    QComboBox,
+    QDoubleSpinBox,
     QLabel,
+    QPushButton,
     QSpinBox,
-    QComboBox,
 )
 
 

diff --git a/brainreg_segment/layout/utils.py b/brainreg_segment/layout/utils.py
@@ -1,61 +1,6 @@
-# Small layout utils
-# import napari
-from napari.viewer import Viewer
-
-import bg_space as bg
-
-# from brainreg_segment.layout.gui_constants import ORIENTATIONS
-
 from qtpy.QtWidgets import QMessageBox
 
 
-def disable_napari_btns(viewer):
-    """
-    Disable some Napari functions to hide them from user interation
-    - Transpose TODO: Understand how to add this properly with space conventions
-    - Grid view
-    - Console
-    - New labels layer
-    - New points layer
-    - New shapes layer
-
-    """
-    viewer.window.qt_viewer.viewerButtons.transposeDimsButton.setVisible(False)
-    viewer.window.qt_viewer.viewerButtons.gridViewButton.setVisible(False)
-    viewer.window.qt_viewer.viewerButtons.consoleButton.setVisible(False)
-    viewer.window.qt_viewer.layerButtons.newLabelsButton.setVisible(False)
-    viewer.window.qt_viewer.layerButtons.newPointsButton.setVisible(False)
-    viewer.window.qt_viewer.layerButtons.newShapesButton.setVisible(False)
-
-
-def disable_napari_key_bindings():
-    """
-    Disable some default key bingings that are unused
-    """
-
-    @Viewer.bind_key("Control-G", overwrite=True)
-    def no_grid_mode_warning(self):
-        print("Grid mode is not supported")
-
-    @Viewer.bind_key("Control-T", overwrite=True)
-    def no_tranpose_warning(self):
-        print("Transposing is not supported")
-
-
-def get_dims_from_origins(origins):
-    """From a list of BG space abbreviations (e.g. ["asl","sla","lsa"]) get correct axes for display in Napari"""
-    all_dims = []
-    for o in range(len(origins)):
-        sc = bg.AnatomicalSpace(origins[0])
-        next_orientation = origins[(o + 1) % len(origins)]
-        dims, flips, _, _ = sc.map_to(next_orientation)
-        assert not any(
-            flips
-        ), f"\nReceived orientations: {origins}\nThese require (orientation) flips. This is not currently supported"
-        all_dims.append(list(dims))
-    return all_dims
-
-
 def display_warning(widget, title, message):
     """
     Display a warning in a pop up that informs
@@ -71,20 +16,3 @@ def display_warning(widget, title, message):
         return True
     else:
         return False
-
-
-# def overwrite_napari_roll(viewer):
-#     """
-#     Overwrite Napari _roll() function with something that makes more sense for a (mouse) brain
-#     Goal: Cycle through views (e.g. asl -> lsa -> sal)
-#     """
-#     dims = get_dims_from_origins(ORIENTATIONS)
-#
-#     def _roll(self):
-#         """Roll order of dimensions for display."""
-#         dims_idx = dims.index(self.order)
-#         next_dims = dims[(dims_idx + 1) % len(dims)]
-#         self.order = next_dims
-#
-#     # Substitute Napari function
-#     napari.components.dims.Dims._roll = _roll
diff --git a/brainreg_segment/measurement/measurement.py b/brainreg_segment/measurement/measurement.py
@@ -4,9 +4,9 @@
 import pathlib
 from typing import List, Tuple
 
-from magicgui import magic_factory
 import napari
 import numpy as np
+from magicgui import magic_factory
 
 
 # For the axis This assumes the following (x,y,z) are each of the following

diff --git a/brainreg_segment/plugins.py b/brainreg_segment/plugins.py
@@ -1,10 +1,11 @@
 from napari_plugin_engine import napari_hook_implementation
-from brainreg_segment.segment import SegmentationWidget
+
 from brainreg_segment.measurement import measurement
 from brainreg_segment.measurement.random_layers import (
     generate_random_points_2d_layer,
     generate_random_points_3d_layer,
 )
+from brainreg_segment.segment import SegmentationWidget
 
 
 @napari_hook_implementation

diff --git a/brainreg_segment/regions/IO.py b/brainreg_segment/regions/IO.py
@@ -1,10 +1,9 @@
-import imio
-import numpy as np
-
 from pathlib import Path
-from skimage import measure
 
+import imio
+import numpy as np
 from imlib.general.pathlib import append_to_pathlib_stem
+from skimage import measure
 
 
 def convert_obj_to_br(verts, faces, voxel_size):

diff --git a/brainreg_segment/regions/analysis.py b/brainreg_segment/regions/analysis.py
@@ -1,13 +1,10 @@
 import numpy as np
 import pandas as pd
-
-
+from imlib.general.list import unique_elements_lists
+from imlib.pandas.misc import initialise_df
 from napari.qt.threading import thread_worker
 from skimage.measure import regionprops_table
 
-from imlib.pandas.misc import initialise_df
-from imlib.general.list import unique_elements_lists
-
 from brainreg_segment.atlas.utils import lateralise_atlas_image
 
 
@@ -66,7 +63,7 @@ def summarise_brain_regions(label_layers, filename, atlas_resolution):
 
     result.columns = ["region"] + [volume_header] + length_columns
 
-    voxel_volume_in_mm = np.prod(atlas_resolution) / (1000 ** 3)
+    voxel_volume_in_mm = np.prod(atlas_resolution) / (1000**3)
 
     result[volume_header] = result[volume_header] * voxel_volume_in_mm
 
@@ -140,7 +137,7 @@ def analyse_region_brain_areas(
     unique_vals_right, counts_right = np.unique(
         annotations_right, return_counts=True
     )
-    voxel_volume_in_mm = np.prod(atlas.resolution) / (1000 ** 3)
+    voxel_volume_in_mm = np.prod(atlas.resolution) / (1000**3)
 
     df = initialise_df(
         "structure_name",

diff --git a/brainreg_segment/regions/layers.py b/brainreg_segment/regions/layers.py
@@ -1,9 +1,9 @@
-import tifffile
-import numpy as np
-
 from glob import glob
 from pathlib import Path
 
+import numpy as np
+import tifffile
+
 
 def add_new_label_layer(
     viewer,

diff --git a/brainreg_segment/segment.py b/brainreg_segment/segment.py
@@ -1,60 +1,37 @@
+from pathlib import Path
+
 import napari
 import numpy as np
-from pathlib import Path
+from bg_atlasapi import BrainGlobeAtlas
 from napari.qt.threading import thread_worker
 from qtpy import QtCore
-
-from qtpy.QtWidgets import (
-    QLabel,
-    QFileDialog,
-    QGridLayout,
-    QGroupBox,
-    QWidget,
-)
-
-from bg_atlasapi import BrainGlobeAtlas
-
-from brainreg_segment.paths import Paths
-
-from brainreg_segment.regions.IO import (
-    save_label_layers,
-    export_label_layers,
-)
-
-from brainreg_segment.tracks.IO import save_track_layers, export_splines
+from qtpy.QtWidgets import QFileDialog, QGridLayout, QGroupBox, QLabel, QWidget
 
 from brainreg_segment.atlas.utils import (
     get_available_atlases,
     structure_from_viewer,
 )
-from brainreg_segment.layout.utils import display_warning
-
-# LAYOUT HELPERS ################################################################################
-
-# from brainreg_segment.layout.utils import (
-#     disable_napari_key_bindings,
-#     disable_napari_btns,
-#     overwrite_napari_roll,
-# )
 from brainreg_segment.layout.gui_constants import (
-    WINDOW_HEIGHT,
-    WINDOW_WIDTH,
+    BOUNDARIES_STRING,
     COLUMN_WIDTH,
-    SEGM_METHODS_PANEL_ALIGN,
+    DISPLAY_REGION_INFO,
     LOADING_PANEL_ALIGN,
-    BOUNDARIES_STRING,
+    SEGM_METHODS_PANEL_ALIGN,
     TRACK_FILE_EXT,
-    DISPLAY_REGION_INFO,
-)
-
-from brainreg_segment.layout.gui_elements import (
-    add_button,
-    add_combobox,
+    WINDOW_HEIGHT,
+    WINDOW_WIDTH,
 )
+from brainreg_segment.layout.gui_elements import add_button, add_combobox
+from brainreg_segment.layout.utils import display_warning
+from brainreg_segment.paths import Paths
+from brainreg_segment.regions.IO import export_label_layers, save_label_layers
 
 # SEGMENTATION  ################################################################################
 from brainreg_segment.segmentation_panels.regions import RegionSeg
 from brainreg_segment.segmentation_panels.tracks import TrackSeg
+from brainreg_segment.tracks.IO import export_splines, save_track_layers
+
+# LAYOUT HELPERS ################################################################################
 
 
 class SegmentationWidget(QWidget):
@@ -68,13 +45,6 @@ def __init__(
         # general variables
         self.viewer = viewer
 
-        # Disable / overwrite napari viewer functions
-        # that either do not make sense or should be avoided by the user
-        # removed for now, to make sure plugin
-        # disable_napari_btns(self.viewer)
-        # disable_napari_key_bindings()
-        # overwrite_napari_roll(self.viewer)
-
         # Main layers
         self.base_layer = []  # Contains registered brain / reference brain
         self.atlas_layer = []  # Contains annotations / region information
@@ -310,7 +280,6 @@ def initialise_atlas(self):
 
         self.status_label.setText("Ready")
         # Set window title
-        # self.viewer.title = f"Atlas: {self.current_atlas_name}"
         self.initialise_segmentation_interface()
         # Check / load previous regions and tracks
         self.region_seg.check_saved_region()
@@ -365,10 +334,12 @@ def get_brainreg_directory(self, standard_space):
         and sets global directory info
         """
         if standard_space:
-            self.plugin = "brainreg-standard"
+            self.plugin = (
+                "brainglobe-napari-io.brainreg_read_dir_standard_space"
+            )
             self.standard_space = True
         else:
-            self.plugin = "brainglobe-io"
+            self.plugin = "brainglobe-napari-io.brainreg_read_dir"
             self.standard_space = False
 
         self.status_label.setText("Loading...")
@@ -440,11 +411,6 @@ def initialise_loaded_data(self):
             self.hemispheres_data = self.viewer.layers["Hemispheres"].data
 
         self.initialise_segmentation_interface()
-
-        # Set window title
-        # self.viewer.title = (
-        #     f"Brainreg: {self.metadata['atlas']} ({self.plugin})"
-        # )
         self.status_label.setText("Ready")
 
     # MORE LAYOUT COMPONENTS ###########################################
@@ -511,10 +477,6 @@ def remove_layers(self):
                 except IndexError:  # no idea why this happens
                     pass
 
-        # There seems to be a napari bug trying to access previously used slider
-        # values. Trying to circument for now
-        self.viewer.window.qt_viewer.dims._last_used = None
-
         self.track_layers = []
         self.label_layers = []
         return True