brainrender 2.1.0__tar.gz → 2.1.2__tar.gz

{brainrender-2.1.0 → brainrender-2.1.2}/.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v4.5.0
       hooks:
           - id: check-docstring-first
           - id: check-executables-have-shebangs
@@ -11,11 +11,11 @@ repos:
             args: [--fix=lf]
           - id: requirements-txt-fixer
           - id: trailing-whitespace
-    - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.0.272
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.1.6
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 23.3.0
+      rev: 23.11.0
       hooks:
           - id: black

{brainrender-2.1.0 → brainrender-2.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: brainrender
-Version: 2.1.0
+Version: 2.1.2
 Summary: Visualisation and exploration of brain atlases and other anatomical data
 Author-email: "Federico Claudi, Adam Tyson, Luigi Petrucco" <hello@brainglobe.info>
 License: BSD-3-Clause
@@ -23,14 +23,14 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: pandas
-Requires-Dist: h5py<=3.9
+Requires-Dist: h5py
 Requires-Dist: vedo>=2023.5.0
 Requires-Dist: k3d
 Requires-Dist: imio
 Requires-Dist: msgpack
 Requires-Dist: pyyaml>=5.3
 Requires-Dist: pooch
-Requires-Dist: morphapi>=0.1.3.0
+Requires-Dist: morphapi>=0.2.1
 Requires-Dist: requests
 Requires-Dist: bg-atlasapi>=1.0.0
 Requires-Dist: tables
@@ -67,7 +67,7 @@ Requires-Dist: PyQt5; extra == "pyqt5"
 
 [![Python Version](https://img.shields.io/pypi/pyversions/brainrender.svg)](https://pypi.org/project/brainrender)
 [![PyPI](https://img.shields.io/pypi/v/brainrender.svg)](https://pypi.org/project/brainrender)
-[![Build Status](https://travis-ci.com/brainglobe/brainrender.svg?branch=master)](https://travis-ci.com/brainglobe/brainrender)
+[![tests](https://github.com/brainglobe/brainrender/workflows/tests/badge.svg)](https://github.com/brainglobe/brainrender/actions)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Coverage Status](https://coveralls.io/repos/github/brainglobe/brainrender/badge.svg)](https://coveralls.io/github/brainglobe/brainrender)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)

{brainrender-2.1.0 → brainrender-2.1.2}/README.md

@@ -6,7 +6,7 @@
 
 [![Python Version](https://img.shields.io/pypi/pyversions/brainrender.svg)](https://pypi.org/project/brainrender)
 [![PyPI](https://img.shields.io/pypi/v/brainrender.svg)](https://pypi.org/project/brainrender)
-[![Build Status](https://travis-ci.com/brainglobe/brainrender.svg?branch=master)](https://travis-ci.com/brainglobe/brainrender)
+[![tests](https://github.com/brainglobe/brainrender/workflows/tests/badge.svg)](https://github.com/brainglobe/brainrender/actions)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Coverage Status](https://coveralls.io/repos/github/brainglobe/brainrender/badge.svg)](https://coveralls.io/github/brainglobe/brainrender)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)

{brainrender-2.1.0 → brainrender-2.1.2}/brainrender/actor.py

@@ -39,7 +39,7 @@ def make_actor_label(
     default_offset = np.array([0, -200, 100])
 
     new_actors = []
-    for n, (actor, label) in enumerate(zip(listify(actors), listify(labels))):
+    for _, (actor, label) in enumerate(zip(listify(actors), listify(labels))):
         # Get label color
         if color is None:
             color = [0.2, 0.2, 0.2]
@@ -74,7 +74,7 @@ def make_actor_label(
     return new_actors
 
 
-class Actor(object):
+class Actor:
     _needs_label = False  # needs to make a label
     _needs_silhouette = False  # needs to make a silhouette
     _is_transformed = False  # has been transformed to correct axes orientation

{brainrender-2.1.0 → brainrender-2.1.2}/brainrender/actors/points.py

@@ -144,5 +144,5 @@ class PointsDensity(Actor):
             .alpha([0, 0.9])
             .mode(1)
         )  # returns a vedo Volume
-        volume.mirror("z")
+
         Actor.__init__(self, volume, name=name, br_class="density")

{brainrender-2.1.0 → brainrender-2.1.2}/brainrender/actors/volume.py

@@ -75,15 +75,22 @@ class Volume(Actor):
 
     def _from_numpy(self, griddata, voxel_size, color, **volume_kwargs):
         """
-        Creates a vedo.Volume actor from a 3D numpy array
-        with volume data
+        Creates a vedo.Volume actor from a 3D numpy array with volume data.
         """
-
-        return VedoVolume(
+        vvol = VedoVolume(
             griddata,
             spacing=[voxel_size, voxel_size, voxel_size],
             **volume_kwargs,
-        ).cmap(color)
+        )
+        vvol.cmap(color)
+        # The transformation below is ALREADY applied
+        # to vedo.Volume instances in render.py
+        # so we should not apply it here.
+        # Flip volume so that it's oriented as in the atlas
+        # vvol.permute_axes(2, 1, 0)
+        # mtx = [[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, -1, 0], [0, 0, 0, 1]]
+        # vvol.apply_transform(mtx)
+        return vvol
 
     def _from_file(self, filepath, voxel_size, color, **volume_kwargs):
         """

{brainrender-2.1.0 → brainrender-2.1.2}/brainrender/camera.py

@@ -1,5 +1,5 @@
-import vtk
 from loguru import logger
+from vtkmodules.vtkRenderingCore import vtkCamera
 
 from brainrender.cameras import cameras
 
@@ -24,14 +24,14 @@ def check_camera_param(camera):
     if isinstance(camera, str):
         return get_camera(camera)
     else:
-        params = ["pos", "viewup", "clippingRange"]
+        params = ["pos", "viewup", "clipping_range"]
         for param in params:
             if param not in list(camera.keys()):
                 raise ValueError(
                     f"Camera parameters dict should include the following keys: {params}, missing: {param}"
                 )
-        if "focalPoint" not in camera.keys():
-            camera["focalPoint"] = None
+        if "focal_point" not in camera.keys():
+            camera["focal_point"] = None
         return camera
 
 
@@ -45,10 +45,10 @@ def set_camera_params(camera, params):
     # Apply camera parameters
     camera.SetPosition(params["pos"])
     camera.SetViewUp(params["viewup"])
-    camera.SetClippingRange(params["clippingRange"])
+    camera.SetClippingRange(params["clipping_range"])
 
-    if "focalPoint" in params.keys() and params["focalPoint"] is not None:
-        camera.SetFocalPoint(params["focalPoint"])
+    if "focal_point" in params.keys() and params["focal_point"] is not None:
+        camera.SetFocalPoint(params["focal_point"])
     if "distance" in params.keys():
         camera.SetDistance(params["distance"])
 
@@ -60,12 +60,11 @@ def set_camera(scene, camera):
     :param scene: instance of Scene
     :param camera: either a string with the name of one of the pre-defined cameras, or
                     a dictionary of camera parameters.
-
     """
     if camera is None:
-        return
+        return None
 
-    if not isinstance(camera, vtk.vtkCamera):
+    if not isinstance(camera, vtkCamera):
         # Get camera params
         camera = check_camera_param(camera)
 
@@ -103,10 +102,10 @@ def get_camera_params(scene=None, camera=None):
 
     params = dict(
         pos=clean(cam.GetPosition()),
-        focalPoint=clean(cam.GetFocalPoint()),
+        focal_point=clean(cam.GetFocalPoint()),
         viewup=clean(cam.GetViewUp()),
         distance=clean(cam.GetDistance()),
-        clippingRange=clean(cam.GetClippingRange()),
+        clipping_range=clean(cam.GetClippingRange()),
         # orientation=clean(cam.GetOrientation()),
     )
     return params

{brainrender-2.1.0 → brainrender-2.1.2}/brainrender/cameras.py

@@ -1,38 +1,38 @@
 sagittal_camera = {
     "pos": (6514, -34, 36854),
     "viewup": (0, -1, 0),
-    "clippingRange": (24098, 49971),
+    "clipping_range": (24098, 49971),
 }
 
 sagittal_camera2 = {
     "pos": (9782, 1795, -40999),
     "viewup": (0, -1, 0),
-    "clippingRange": (23256, 51031),
+    "clipping_range": (23256, 51031),
 }
 
 
 frontal_camera = {
     "pos": (-19199, -1428, -5763),
     "viewup": (0, -1, 0),
-    "clippingRange": (19531, 40903),
+    "clipping_range": (19531, 40903),
 }
 
 top_camera = {
     "pos": (7760, -31645, -5943),
     "viewup": (-1, 0, 0),
-    "clippingRange": (27262, 45988),
+    "clipping_range": (27262, 45988),
 }
 
 top_side_camera = {
     "pos": (4405, -31597, -5411),
     "viewup": (0, 0, -1),
-    "clippingRange": (26892, 46454),
+    "clipping_range": (26892, 46454),
 }
 
 three_quarters_camera = {
     "pos": (-20169, -7298, 14832),
     "viewup": (0, -1, 0),
-    "clippingRange": (16955, 58963),
+    "clipping_range": (16955, 58963),
 }
 
 cameras = dict(

{brainrender-2.1.0 → brainrender-2.1.2}/brainrender/render.py

@@ -1,7 +1,6 @@
 from datetime import datetime
 from pathlib import Path
 
-import matplotlib.pyplot as plt
 import numpy as np
 from loguru import logger
 from myterial import amber, deep_purple_light, orange, teal
@@ -55,7 +54,7 @@ class Render:
             title="brainrender",
             bg=settings.BACKGROUND_COLOR,
             offscreen=settings.OFFSCREEN,
-            size="full" if settings.WHOLE_SCREEN else "auto",
+            size="full" if settings.WHOLE_SCREEN else (1600, 1200),
         )
 
         self.plotter.keyPressFunction = self.keypress
@@ -135,6 +134,9 @@ class Render:
                 if isinstance(actor._mesh, VedoVolume):
                     actor._mesh.permute_axes(2, 1, 0)
                     actor._mesh.apply_transform(mtx, True)
+                    actor._mesh.transform = (
+                        None  # otherwise it gets applied twice
+                    )
                 elif actor.br_class in ["None", "Gene Data"]:
                     actor._mesh.apply_transform(mtx_swap_x_z)
                     actor._mesh.apply_transform(mtx)
@@ -153,7 +155,6 @@ class Render:
                     logger.debug(
                         f'Failed to reverse actor: "{actor.name} (type: {actor.br_class})"'
                     )
-                    pass
                 actor._is_transformed = True
 
         # Add silhouette and labels
@@ -224,8 +225,8 @@ class Render:
         else:
             camera = check_camera_param(camera)
 
-        if "focalPoint" not in camera.keys() or camera["focalPoint"] is None:
-            camera["focalPoint"] = self.root._mesh.center_of_mass()
+        if "focal_point" not in camera.keys() or camera["focal_point"] is None:
+            camera["focal_point"] = self.root._mesh.center_of_mass()
 
         if not self.backend and camera is not None:
             camera = set_camera(self, camera)
@@ -290,7 +291,7 @@ class Render:
             )
 
     def close(self):
-        plt.close()
+        self.plotter.close()
 
     def export(self, savepath):
         """
@@ -362,7 +363,7 @@ class Render:
     def _print_camera(self):
         pms = get_camera_params(scene=self)
 
-        focal = pms.pop("focalPoint", None)
+        focal = pms.pop("focal_point", None)
         dst = pms.pop("distance", None)
 
         names = [
@@ -375,7 +376,7 @@ class Render:
             *names,
             f"[{orange}]   }}",
             f"[{deep_purple_light}]Additional, (optional) parameters:",
-            f"[green bold]     'focalPoint'[/green bold]: [{amber}]{focal},",
+            f"[green bold]     'focal_point'[/green bold]: [{amber}]{focal},",
             f"[green bold]     'distance'[/green bold]: [{amber}]{dst},",
             sep="\n",
         )
@@ -390,7 +391,7 @@ class Render:
         if key == "s":
             self.screenshot()
 
-        elif key == "q" or key == "Esc":
+        elif key in ("q", "Esc"):
             self.close()
 
         elif key == "c":

{brainrender-2.1.0 → brainrender-2.1.2}/brainrender/scene.py

@@ -70,9 +70,7 @@ class Scene(JupyterMixIn, Render):
             "root",
             alpha=settings.ROOT_ALPHA,
             color=settings.ROOT_COLOR,
-            silhouette=True
-            if root and settings.SHADER_STYLE == "cartoon"
-            else False,
+            silhouette=bool(root and settings.SHADER_STYLE == "cartoon"),
         )
         self.atlas.root = self.root  # give atlas access to root
         self._root_mesh = self.root.mesh.clone()
@@ -108,7 +106,7 @@ class Scene(JupyterMixIn, Render):
         Creates a small inset showing the brain's orientation
         """
         if settings.OFFSCREEN:
-            return None
+            return
 
         inset = self._root_mesh.clone()
         inset.alpha(1)  # scale(0.5)
@@ -401,7 +399,7 @@ class Scene(JupyterMixIn, Render):
                 f"[bold][{amber}]- {act.name}[/bold][{orange_darker}] (type: [{orange}]{act.br_class}[/{orange}])"
             )
 
-        if "win32" != sys.platform:
+        if sys.platform != "win32":
             actors.print()
         else:
             print(pi.utils.stringify(actors, maxlen=-1))

{brainrender-2.1.0 → brainrender-2.1.2}/brainrender/settings.py

@@ -17,8 +17,6 @@ vsettings.max_number_of_peels = 12
 vsettings.occlusion_ratio = 0.1
 vsettings.multi_samples = 0 if sys.platform == "darwin" else 8
 
-# vsettings.useSSAO = True
-
 # For transparent background with screenshots
 vsettings.screenshot_transparent_background = False  # vedo for transparent bg
 vsettings.use_fxaa = False
@@ -36,5 +34,5 @@ ROOT_ALPHA = 0.2  # transparency of the overall brain model's actor'
 SCREENSHOT_SCALE = 1
 SHADER_STYLE = "cartoon"  # affects the look of rendered brain regions: [metallic, plastic, shiny, glossy]
 SHOW_AXES = True
-WHOLE_SCREEN = True  # If true render window is full screen
+WHOLE_SCREEN = False  # If true render window is full screen
 OFFSCREEN = False

{brainrender-2.1.0 → brainrender-2.1.2}/brainrender/video.py

@@ -200,6 +200,10 @@ class Animation(VideoMaker):
         self.keyframes[0] = dict(  # make sure first frame is a keyframe
             zoom=None, camera=None, callback=None
         )
+        self.keyframes_numbers = 0
+        self.nframes = 0
+        self.last_keyframe = 0
+        self.segment_fact = 0
 
     def add_keyframe(
         self,

{brainrender-2.1.0 → brainrender-2.1.2}/brainrender.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: brainrender
-Version: 2.1.0
+Version: 2.1.2
 Summary: Visualisation and exploration of brain atlases and other anatomical data
 Author-email: "Federico Claudi, Adam Tyson, Luigi Petrucco" <hello@brainglobe.info>
 License: BSD-3-Clause
@@ -23,14 +23,14 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: pandas
-Requires-Dist: h5py<=3.9
+Requires-Dist: h5py
 Requires-Dist: vedo>=2023.5.0
 Requires-Dist: k3d
 Requires-Dist: imio
 Requires-Dist: msgpack
 Requires-Dist: pyyaml>=5.3
 Requires-Dist: pooch
-Requires-Dist: morphapi>=0.1.3.0
+Requires-Dist: morphapi>=0.2.1
 Requires-Dist: requests
 Requires-Dist: bg-atlasapi>=1.0.0
 Requires-Dist: tables
@@ -67,7 +67,7 @@ Requires-Dist: PyQt5; extra == "pyqt5"
 
 [![Python Version](https://img.shields.io/pypi/pyversions/brainrender.svg)](https://pypi.org/project/brainrender)
 [![PyPI](https://img.shields.io/pypi/v/brainrender.svg)](https://pypi.org/project/brainrender)
-[![Build Status](https://travis-ci.com/brainglobe/brainrender.svg?branch=master)](https://travis-ci.com/brainglobe/brainrender)
+[![tests](https://github.com/brainglobe/brainrender/workflows/tests/badge.svg)](https://github.com/brainglobe/brainrender/actions)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Coverage Status](https://coveralls.io/repos/github/brainglobe/brainrender/badge.svg)](https://coveralls.io/github/brainglobe/brainrender)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)

{brainrender-2.1.0 → brainrender-2.1.2}/brainrender.egg-info/requires.txt

@@ -1,13 +1,13 @@
 numpy
 pandas
-h5py<=3.9
+h5py
 vedo>=2023.5.0
 k3d
 imio
 msgpack
 pyyaml>=5.3
 pooch
-morphapi>=0.1.3.0
+morphapi>=0.2.1
 requests
 bg-atlasapi>=1.0.0
 tables

{brainrender-2.1.0 → brainrender-2.1.2}/pyproject.toml

@@ -9,14 +9,14 @@ dynamic = ["version"]
 dependencies = [
     "numpy",
     "pandas",
-    "h5py<=3.9", # vedo requires hdf5 <=1.12.x but hdf5 is 1.14+ from h5py 3.10 onwards
+    "h5py",
     "vedo>=2023.5.0",
     "k3d",
     "imio",
     "msgpack",
     "pyyaml>=5.3",
     "pooch",
-    "morphapi>=0.1.3.0",
+    "morphapi>=0.2.1",
     "requests",
     "bg-atlasapi>=1.0.0",
     "tables",