rapidtide 2.9.5__py3-none-any.whl → 3.1.3__py3-none-any.whl

rapidtide-2.9.5.data/scripts/spectrogram

@@ -1,23 +0,0 @@
-#!python
-# -*- coding: utf-8 -*-
-#
-#   Copyright 2016-2024 Blaise Frederick
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-#
-#
-import rapidtide.workflows.parser_funcs as pf
-import rapidtide.workflows.spectrogram as theworkflow
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.spectrogram)

rapidtide-2.9.5.data/scripts/synthASL

@@ -1,23 +0,0 @@
-#!python
-# -*- coding: utf-8 -*-
-#
-#   Copyright 2016-2024 Blaise Frederick
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-#
-#
-import rapidtide.workflows.parser_funcs as pf
-import rapidtide.workflows.synthASL as theworkflow
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.synthASL)

rapidtide-2.9.5.data/scripts/tcfrom2col

@@ -1,23 +0,0 @@
-#!python
-# -*- coding: utf-8 -*-
-#
-#   Copyright 2016-2024 Blaise Frederick
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-#
-#
-import rapidtide.workflows.parser_funcs as pf
-import rapidtide.workflows.tcfrom2col as theworkflow
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.tcfrom2col)

rapidtide-2.9.5.data/scripts/tcfrom3col

@@ -1,23 +0,0 @@
-#!python
-# -*- coding: utf-8 -*-
-#
-#   Copyright 2016-2024 Blaise Frederick
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-#
-#
-import rapidtide.workflows.parser_funcs as pf
-import rapidtide.workflows.tcfrom3col as theworkflow
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.tcfrom3col)

rapidtide-2.9.5.data/scripts/temporaldecomp

@@ -1,23 +0,0 @@
-#!python
-# -*- coding: utf-8 -*-
-#
-#   Copyright 2016-2024 Blaise Frederick
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-#
-#
-import rapidtide.workflows.niftidecomp as theworkflow
-import rapidtide.workflows.parser_funcs as pf
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser_temporal, theworkflow.main_temporal)

rapidtide-2.9.5.data/scripts/threeD

@@ -1,236 +0,0 @@
-#!python
-# -*- coding: utf-8 -*-
-#
-#   Copyright 2016-2024 Blaise Frederick
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-#
-#
-
-# -----------------------------------------------------------------------------
-# Copyright (c) Vispy Development Team. All Rights Reserved.
-# Distributed under the (new) BSD License. See LICENSE.txt for more info.
-# -----------------------------------------------------------------------------
-# vispy: gallery 2
-
-"""
-Example volume rendering
-Controls:
-* 1  - toggle camera between first person (fly), regular 3D (turntable) and
-       arcball
-* 2  - toggle between volume rendering methods
-* 3  - toggle between stent-CT / brain-MRI image
-* 4  - toggle between colormaps
-* 0  - reset cameras
-* [] - decrease/increase isosurface threshold
-With fly camera:
-* WASD or arrow keys - move around
-* SPACE - brake
-* FC - move up-down
-* IJKL or mouse - look around
-"""
-
-import os
-import sys
-from itertools import cycle
-
-import numpy as np
-from vispy import app, scene
-from vispy.color import BaseColormap, get_colormaps
-from vispy.visuals.transforms import STTransform
-
-import rapidtide.io as tide_io
-import rapidtide.stats as tide_stats
-
-
-def usage():
-    print(os.path.basename(sys.argv[0]), "- render 3 (or 4) d images")
-    print("")
-    print("usage: ", os.path.basename(sys.argv[0]), " niftifile")
-    print("")
-    print("required arguments:")
-    print("    niftifile:                3 or 4 dimensional nifti file containing MR data")
-    print("")
-    # print("optional arguments:")
-    # print("    --debug                    - turn on debugging messages")
-    # print("    --glm                      - generate voxelwise aliased synthetic cardiac regressors and filter them out")
-
-
-def incrementvolume(volumelist):
-    global activevol
-
-    volumelist[activevol].visible = False
-    activevol = (activevol + 1) % len(volumelist)
-    volumelist[activevol].visible = True
-
-
-### control flow starts here
-global activevol
-activevol = 0
-
-nargs = len(sys.argv)
-if nargs < 2:
-    usage()
-    exit()
-thefilename = sys.argv[1]
-
-# Read volume
-nim, nim_data, nim_hdr, thedims, thesizes = tide_io.readfromnifti(thefilename)
-xsize, ysize, numslices, timepoints = tide_io.parseniftidims(thedims)
-xdim, ydim, slicethickness, tr = tide_io.parseniftisizes(thesizes)
-vollist = []
-if timepoints > 1:
-    for i in range(timepoints):
-        vollist.append(np.swapaxes(nim_data[:, :, :, i], 0, 2))
-else:
-    vollist.append(np.swapaxes(nim_data[:, :, :], 0, 2))
-
-# Prepare canvas
-canvas = scene.SceneCanvas(keys="interactive", size=(800, 600), show=True)
-canvas.measure_fps()
-
-# Set up a viewbox to display the image with interactive pan/zoom
-view = canvas.central_widget.add_view()
-
-# Set whether we are emulating a 3D texture
-emulate_texture = False
-
-# Create the volume visuals, only one is visible
-minsize = np.min([xdim, ydim, slicethickness])
-volumelist = []
-transfacs = (0, 0, 0)
-scalefacs = (xdim / minsize, ydim / minsize, slicethickness / minsize)
-datarobustmax = tide_stats.getfracvals(nim_data, [0.98])[0]
-fracval = 0.2
-clims = (datarobustmax * fracval, 2.0 * datarobustmax)
-
-for thevol in vollist:
-    volumelist.append(
-        scene.visuals.Volume(
-            thevol,
-            parent=view.scene,
-            threshold=0.2,
-            emulate_texture=emulate_texture,
-            clim=clims,
-        )
-    )
-    volumelist[-1].transform = scene.STTransform(translate=transfacs)
-    volumelist[-1].transform = scene.STTransform(scale=scalefacs)
-    volumelist[-1].visible = False
-volumelist[activevol].visible = True
-
-# Create three cameras (Fly, Turntable and Arcball)
-fov = 60.0
-cam1 = scene.cameras.FlyCamera(parent=view.scene, fov=fov, name="Fly")
-cam2 = scene.cameras.TurntableCamera(parent=view.scene, fov=fov, name="Turntable")
-cam3 = scene.cameras.ArcballCamera(parent=view.scene, fov=fov, name="Arcball")
-view.camera = cam2  # Select turntable at first
-
-# Create an XYZAxis visual
-axis = scene.visuals.XYZAxis(parent=view)
-s = STTransform(translate=(50, 50), scale=(50, 50, 50, 1))
-affine = s.to_numpy()
-axis.transform = affine
-
-
-# create colormaps that work well for translucent and additive volume rendering
-class TransFire(BaseColormap):
-    glsl_map = """
-    vec4 translucent_fire(float t) {
-        return vec4(pow(t, 0.5), t, t*t, max(0, t*1.05 - 0.05));
-    }
-    """
-
-
-class TransGrays(BaseColormap):
-    glsl_map = """
-    vec4 translucent_grays(float t) {
-        return vec4(t, t, t, t*0.05);
-    }
-    """
-
-
-# Setup colormap iterators
-opaque_cmaps = cycle(get_colormaps())
-translucent_cmaps = cycle([TransFire(), TransGrays()])
-opaque_cmap = next(opaque_cmaps)
-translucent_cmap = next(translucent_cmaps)
-
-
-# Implement axis connection with cam2
-@canvas.events.mouse_move.connect
-def on_mouse_move(event):
-    if event.button == 1 and event.is_dragging:
-        axis.transform.reset()
-
-        axis.transform.rotate(cam2.roll, (0, 0, 1))
-        axis.transform.rotate(cam2.elevation, (1, 0, 0))
-        axis.transform.rotate(cam2.azimuth, (0, 1, 0))
-
-        axis.transform.scale((50, 50, 0.001))
-        axis.transform.translate((50.0, 50.0))
-        axis.update()
-
-
-# Implement key presses
-@canvas.events.key_press.connect
-def on_key_press(event):
-    global opaque_cmap, translucent_cmap, activevol
-    if event.text == "1":
-        cam_toggle = {cam1: cam2, cam2: cam3, cam3: cam1}
-        view.camera = cam_toggle.get(view.camera, cam2)
-        print(view.camera.name + " camera")
-        if view.camera is cam2:
-            axis.visible = True
-        else:
-            axis.visible = False
-    elif event.text == "2":
-        methods = ["mip", "translucent", "iso", "additive"]
-        method = methods[(methods.index(volumelist[activevol].method) + 1) % 4]
-        print("Volume render method: %s" % method)
-        cmap = opaque_cmap if method in ["mip", "iso"] else translucent_cmap
-        for thevolume in volumelist:
-            thevolume.method = method
-            thevolume.cmap = cmap
-    elif event.text == "3":
-        incrementvolume(volumelist)
-        # volumelist[activevol].visible = False
-        # activevol = (activevol + 1) % len(volumelist)
-        # print('activevol set to', activevol)
-        # volumelist[activevol].visible = True
-    elif event.text == "4":
-        if volumelist[activevol].method in ["mip", "iso"]:
-            cmap = opaque_cmap = next(opaque_cmaps)
-        else:
-            cmap = translucent_cmap = next(translucent_cmaps)
-        for thevolume in volumelist:
-            thevolume.cmap = cmap
-    elif event.text == "0":
-        cam1.set_range()
-        cam3.set_range()
-    elif event.text != "" and event.text in "[]":
-        s = -0.025 if event.text == "[" else 0.025
-        for thevolume in volumelist:
-            thevolume.threshold += s
-        th = volumelist[activevol].threshold
-        print("Isosurface threshold: %0.3f" % th)
-
-
-# for testing performance
-# @canvas.connect
-# def on_draw(ev):
-# canvas.update()
-
-if __name__ == "__main__":
-    print(__doc__)
-    app.run()

rapidtide-2.9.5.data/scripts/tidepool

@@ -1,23 +0,0 @@
-#!python
-# -*- coding: utf-8 -*-
-#
-#   Copyright 2016-2024 Blaise Frederick
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-#
-#
-import rapidtide.workflows.parser_funcs as pf
-import rapidtide.workflows.tidepool as theworkflow
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.tidepool)

rapidtide-2.9.5.data/scripts/variabilityizer

@@ -1,23 +0,0 @@
-#!python
-# -*- coding: utf-8 -*-
-#
-#   Copyright 2016-2024 Blaise Frederick
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-#
-#
-import rapidtide.workflows.parser_funcs as pf
-import rapidtide.workflows.variabilityizer as theworkflow
-
-if __name__ == "__main__":
-    pf.generic_init(theworkflow._get_parser, theworkflow.variabilityizer)