Brainrender 1.0.0.0 bug fixes (#45)

* remove brainrender.Utils.image dependency

* flake8 compatibility

* add verison to init

* fix manual_seg

* slim down testing matrix

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+repos:
+-   repo: https://github.com/python/black
+    rev: 19.10b0
+    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

.travis.yml

@@ -24,27 +24,13 @@ jobs:
       dist: bionic
       python: 3.7
       script: travis_wait 40 bash travis/install_test_linux.sh
-    - stage: test
-      name: "Ubuntu Xenial python 3.6"
-      language: python
-      os: linux
-      dist: xenial
-      python: 3.6
-      script: travis_wait 40 bash travis/install_test_linux.sh
     - stage: test
       name: "Ubuntu Xenial python 3.7"
       language: python
       os: linux
       dist: xenial
       python: 3.7
       script: travis_wait 40 bash travis/install_test_linux.sh
-    - stage: test
-      name: "Windows Python 3.6"
-      language: shell
-      env: TRAVIS_PYTHON_VERSION=3.6
-      os: windows
-      before_install: source travis/install_windows.sh
-      script: travis_wait 40 bash travis/test_windows.sh
     - stage: test
       name: "Windows Python 3.7"
       language: shell
@@ -53,12 +39,6 @@ jobs:
       before_install:
         - source travis/install_windows.sh
       script: travis_wait 40 bash travis/test_windows.sh
-    - stage: test
-      name: "macOS Python 3.6"
-      os: osx
-      language: shell
-      env: TRAVIS_PYTHON_VERSION=3.6
-      script: travis_wait 40 bash travis/install_test_osx.sh
     - stage: test
       name: "macOS Python 3.7"
       os: osx

neuro/__init__.py

@@ -0,0 +1,2 @@
+__author__ = "Adam Tyson"
+__version__ = "0.0.18"

neuro/segmentation/manual_segmentation/widgets.py

@@ -28,7 +28,13 @@
     add_new_region_layer,
     view_in_brainrender,
 )
-from neuro.gui.elements import *
+from neuro.gui.elements import (
+    add_button,
+    add_checkbox,
+    add_float_box,
+    add_int_box,
+    add_combobox,
+)
 
 from qtpy.QtWidgets import (
     QLabel,
@@ -451,7 +457,9 @@ def run_region_analysis(self):
     def initialise_brainrender(self):
         self.scene = Scene(add_root=True)
         self.splines = None
-        self.available_meshes = [""] + self.scene.atlas.all_avaliable_meshes
+        self.available_meshes = [""] + list(
+            self.scene.atlas.lookup_df["acronym"]
+        )
 
     def to_brainrender(self):
         print("Closing viewer and viewing in brainrender.")

neuro/visualise/brainrender_tools.py

@@ -1,6 +1,5 @@
 import numpy as np
 from pathlib import Path
-from brainrender.Utils.image import reorient_image, marching_cubes_to_obj
 from brainrender.scene import Scene
 from skimage import measure
 
@@ -12,6 +11,51 @@
 )
 
 
+def marching_cubes_to_obj(marching_cubes_out, output_file):
+    """
+    Saves the output of skimage.measure.marching_cubes as an .obj file
+    :param marching_cubes_out: tuple
+    :param output_file: str
+    """
+
+    verts, faces, normals, _ = marching_cubes_out
+    with open(output_file, "w") as f:
+        for item in verts:
+            f.write(f"v {item[0]} {item[1]} {item[2]}\n")
+        for item in normals:
+            f.write(f"vn {item[0]} {item[1]} {item[2]}\n")
+        for item in faces:
+            f.write(
+                f"f {item[0]}//{item[0]} {item[1]}//{item[1]} "
+                f"{item[2]}//{item[2]}\n"
+            )
+        f.close()
+
+
+def reorient_image(image, invert_axes=None, orientation="saggital"):
+    """
+    Reorients the image to the coordinate space of the atlas
+    :param image_path: str
+    :param threshold: float
+    :param invert_axes: tuple (Default value = None)
+    :param image:
+    :param orientation:  (Default value = "saggital")
+    """
+    # TODO: move this to brainio
+    if invert_axes is not None:
+        for axis in invert_axes:
+            image = np.flip(image, axis=axis)
+
+    if orientation != "saggital":
+        if orientation == "coronal":
+            transposition = (2, 1, 0)
+        elif orientation == "horizontal":
+            transposition = (1, 2, 0)
+
+        image = np.transpose(image, transposition)
+    return image
+
+
 def render_region_from_custom_atlas(
     output_dir,
     atlas_ids,
@@ -35,7 +79,7 @@ def render_region_from_custom_atlas(
         oriented_binary, 0, step_size=1
     )
 
-    if voxel_size is not 1:
+    if voxel_size != 1:
         verts = verts * voxel_size
 
     faces = faces + 1
@@ -94,7 +138,7 @@ def extract_and_save_object(
 
 
 def convert_obj_to_br(verts, faces, voxel_size=10):
-    if voxel_size is not 1:
+    if voxel_size != 1:
         verts = verts * voxel_size
 
     faces = faces + 1

neuro/visualise/viewer.py

@@ -6,7 +6,6 @@
 from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
 from qtpy import QtCore
 from qtpy.QtWidgets import (
-    QLabel,
     QFileDialog,
     QGridLayout,
     QWidget,

pyproject.toml

@@ -0,0 +1,16 @@
+[tool.black]
+line-length = 79
+include = '\.pyi?$'
+exclude = '''
+/(
+    \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | _build
+  | buck-out
+  | build
+  | dist
+)/
+'''

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+addopts = --cov=neuro
+markers =
+    slow: marks tests as slow (deselect with '-m "not slow"')

setup.cfg

@@ -0,0 +1,17 @@
+[bumpversion]
+current_version = 0.0.18
+commit = True
+tag = True
+
+[bumpversion:file:setup.py]
+search = version="{current_version}"
+replace = version="{new_version}"
+
+[bumpversion:file:neuro/__init__.py]
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"
+
+[flake8]
+ignore = E203, E231, W503, E501
+max-line-length = 79
+exclude = __init__.py

setup.py

@@ -14,11 +14,20 @@
 
 setup(
     name="neuro",
-    version="0.0.16",
+    version="0.0.18",
     description="Visualisation and analysis of brain imaging data",
     install_requires=requirements,
     extras_require={
-        "dev": ["black", "pytest-cov", "pytest", "gitpython", "coverage",]
+        "dev": [
+            "black",
+            "pytest-cov",
+            "pytest",
+            "gitpython",
+            "coverage",
+            "bump2version",
+            "pre-commit",
+            "flake8",
+        ]
     },
     python_requires=">=3.6, <3.8",
     packages=find_namespace_packages(exclude=("docs", "tests*")),