pyfast 4.12.0__cp36-abi3-manylinux1_x86_64.whl

fast/README.md

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+![](https://github.com/smistad/FAST/wiki/images/fast_logo.png)
+
+FAST (Framework for Heterogeneous Medical Image Computing and Visualization) is an open-source cross-platform framework with the main goal of making it easier to do high performance processing and visualization of medical images on heterogeneous systems utilizing both multi-core CPUs and GPUs. To achieve this, FAST is constructed using modern C++, OpenCL and OpenGL.
+
+To start using the framework, please see the [project wiki](https://github.com/smistad/FAST/wiki/). To run the examples in this release download the [test data](https://github.com/smistad/FAST/wiki/Test-data) and put it in the same folder as this readme.
+
+FAST has been described in the following research articles. If you use this framework for research please cite them:
+
+*[FAST: framework for heterogeneous medical image computing and visualization](http://www.eriksmistad.no/wp-content/uploads/FAST_framework_for_heterogeneous_medical_image_computing_and_visualization.pdf)  
+Erik Smistad, Mohammadmehdi Bozorgi, Frank Lindseth  
+International Journal of Computer Assisted Radiology and Surgery 2015*
+
+*[High Performance Neural Network Inference, Streaming, and Visualization of Medical Images Using FAST](https://www.eriksmistad.no/wp-content/uploads/High-Performance-Neural-Network-Inference-Streaming-and-Visualization-of-Medical-Images-Using-FAST.pdf)  
+Erik Smistad, Andreas Østvik, André Pedersen  
+IEEE Access 2019*
+
+[![Join the chat at https://gitter.im/smistad/FAST](https://badges.gitter.im/smistad/FAST.svg)](https://gitter.im/smistad/FAST?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+
+
+Licenses
+=========================
+This FAST release is bundled with the following third-party software:
+
+* [Qt5](https://www.qt.io)
+* [Eigen](http://eigen.tuxfamily.org)
+* [Eigen SWIG interface (BSD 3-clause)](https://github.com/Biomechanical-ToolKit/BTKCore/blob/master/Utilities/SWIG/eigen.i)
+* [zlib](http://www.zlib.net)
+* [OpenIGTLink](http://openigtlink.org)
+* [NumPy](http://www.numpy.org)
+* [Semaphore C++11 implementation by Jeff Preshing](https://github.com/preshing/cpp11-on-multicore)
+* [DCMTK](https://github.com/DCMTK/dcmtk)
+* [TensorFlow (Apache 2.0)](http://tensorflow.org)
+* [Clarius Ultrasound Listener API (BSD 3-clause)](https://github.com/clariusdev/listener)
+* [OpenSlide](https://openslide.org)
+* [TIFF](http://www.libtiff.org/)
+* [RealSense](https://github.com/IntelRealSense/librealsense)
+* [OpenVINO (Apache 2.0)](http://github.com/opencv/dldt) which uses [TBB (Apache 2.0)](https://github.com/intel/tbb), [clDNN (Apache 2.0)](https://github.com/intel/cldnn), [MKL-DNN (Apache 2.0)](https://github.com/intel/mkl-dnn), [ADE (Apache 2.0)](https://github.com/opencv/ade), [pugixml (MIT)](https://pugixml.org/) and the [G-API (fluid) code from OpenCV (BSD 3-clause)](https://github.com/opencv/opencv/wiki/Graph-API)
+* [hdf5](https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5/browse)
+* [JKQtPlotter (LGPL 2.1)](https://github.com/jkriege2/JKQtPlotter)
+
+The license of each software can be found in the licenses folder.

fast/__init__.py

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+# Check that user is importing FAST in main thread, which is necessary for Qt
+import threading
+if threading.current_thread() != threading.main_thread():
+    raise ImportError('FAST must be imported in main thread (import fast)!')
+
+import os
+import sys
+is_windows = sys.platform.startswith('win')
+# Set base path in config to be two directories up from where the python module is
+bin_path = path = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'bin'))
+if is_windows:
+    path = bin_path
+else:
+    path = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'lib'))
+sys.path.append(path) # This is needed to find _fast binary python extension
+os.environ['PATH'] = path + os.pathsep + os.environ['PATH'] # This is needed in order for C++ to dynamically load DLLs
+
+from .fast import *
+fast.Config.setBasePath(bin_path)
+fast.Config.setTerminateHandlerDisabled(True)
+if True not in [x in sys.argv[0] for x in ['UFFviewer', 'runPipeline', 'systemCheck']]:
+    fast.ImageFileImporter.create('') # Trigger splash, GL context initialization etc.

fast/bin/fast_configuration.txt

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+## FAST Configuration file
+#TestDataPath = /path/to/data/
+#KernelSourcePath = /path/to/kernel/source/FAST/
+#KernelBinaryPath = /path/to/kernel/binary/
+#DocumentationPath = /path/to/doc/
+#PipelinePath = /path/to/pipeline/
+
+#TestDataPath = @ROOT@/data/
+KernelSourcePath = @ROOT@/kernels/
+KernelBinaryPath = @ROOT@/kernel_binaries/
+DocumentationPath = @ROOT@/doc/
+PipelinePath = @ROOT@/pipelines/
+LibraryPath = @ROOT@/lib/
+QtPluginsPath = @ROOT@/plugins/

fast/doc/bright-plotting-style.ini

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+[plots]
+widget_background_color=#FFFFFF
+widget_background_color_for_export=#FFFFFF
+plot_background_color=#FFFFFF
+graphs\graphs_base\linewidth=3
+graphs\graphs_base\symbol_size=0
+graphs\graphs_base\symbol_line_width=0.75
+graphs\graphs_base\symbol_fill_color_mode=lighter
+graphs\graphs_base\error_color_mode=lighter
+graphs\graphs_barchart\linewidth=0
+graphs\graphs_barchart\fill_color_mode=same
+graphs\graphs_boxplot\graph_color_mode=same_non_transparent
+graphs\graphs_filled\fill_color_mode=more_transparent
+graphs\graphs_geometric\color=black
+graphs\graphs_annotation\color=black
+graphs\graphs_annotation\text_color=black
+text_default_color=#0A0A0A
+plot_frame_color=#0A0A0A
+key\frame_color=#0A0A0A
+key\background_color=#CCCCCC
+key\text_color=#0A0A0A
+axis_x\color=#000000
+axis_x\line_width=1
+axis_x\grid\style=dash
+axis_x\grid\color=#0A0A0A
+axis_x\minor_grid\color=#0A0A0A
+axis_x\minor_tick\inside_length=2
+axis_x\minor_tick\outside_length=2
+axis_x\ticks\width=1
+axis_x\zero_line\line_width=1
+axis_x\zero_line\color=#0A0A0A
+axis_y\color=#0A0A0A
+axis_y\line_width=1
+axis_y\grid\color=#0A0A0A
+axis_y\grid\style=dash
+axis_y\minor_grid\color=#0A0A0A
+axis_y\minor_tick\inside_length=2
+axis_y\minor_tick\outside_length=2
+axis_y\ticks\width=1
+axis_y\zero_line\line_width=1
+axis_y\zero_line\color=#0A0A0A
+axis_colorbar_right\color=#0A0A0A
+axis_colorbar_right\draw_mode2=line+ticks+labels+axislabel
+axis_colorbar_right\line_width=1
+axis_colorbar_right\grid\color=#0A0A0A
+axis_colorbar_right\minor_tick\inside_length=2
+axis_colorbar_right\minor_tick\outside_length=2
+axis_colorbar_right\ticks\width=1
+axis_colorbar_right\zero_line\line_width=1
+axis_colorbar_right\zero_line\color=#0A0A0A
+axis_colorbar_top\color=#0A0A0A
+axis_colorbar_top\line_width=1
+axis_colorbar_top\grid\color=#0A0A0A
+axis_colorbar_top\minor_tick\inside_length=2
+axis_colorbar_top\minor_tick\outside_length=2
+axis_colorbar_top\ticks\width=1
+axis_colorbar_top\zero_line\line_width=1
+axis_colorbar_top\zero_line\color=#0A0A0A
+graphs\auto_styles\color0="#3DFF00,80%"
+graphs\auto_styles\color1="#FF3D00,80%"
+graphs\auto_styles\color2="#FF3D00,80%"
+graphs\auto_styles\color3="#FFEB3B,80%"
+graphs\auto_styles\color4="#FF9800,80%"
+graphs\auto_styles\color5="#9C27B0,80%"
+graphs\auto_styles\color6="#29B6F6,80%"
+graphs\auto_styles\color7="blue,80%"

fast/doc/dark-plotting-style.ini

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+[plots]
+widget_background_color=#000000
+widget_background_color_for_export=#000000
+plot_background_color=#000000
+graphs\graphs_base\linewidth=3
+graphs\graphs_base\symbol_size=0
+graphs\graphs_base\symbol_line_width=0.75
+graphs\graphs_base\symbol_fill_color_mode=darker
+graphs\graphs_base\error_color_mode=lighter
+graphs\graphs_barchart\linewidth=0
+graphs\graphs_barchart\fill_color_mode=same
+graphs\graphs_boxplot\graph_color_mode=same_non_transparent
+graphs\graphs_filled\fill_color_mode=more_transparent
+graphs\graphs_geometric\color=white
+graphs\graphs_annotation\color=white
+graphs\graphs_annotation\text_color=white
+text_default_color=#FAFAFA
+plot_frame_color=#FAFAFA
+key\frame_color=#FAFAFA
+key\background_color=#424242
+key\text_color=#FAFAFA
+axis_x\color=#000000
+axis_x\line_width=1
+axis_x\grid\style=dash
+axis_x\grid\color=#616161
+axis_x\minor_grid\color=#616161
+axis_x\minor_tick\inside_length=2
+axis_x\minor_tick\outside_length=2
+axis_x\ticks\width=1
+axis_x\zero_line\line_width=1
+axis_x\zero_line\color=#FAFAFA
+axis_y\color=#FAFAFA
+axis_y\line_width=1
+axis_y\grid\color=#616161
+axis_y\grid\style=dash
+axis_y\minor_grid\color=#616161
+axis_y\minor_tick\inside_length=2
+axis_y\minor_tick\outside_length=2
+axis_y\ticks\width=1
+axis_y\zero_line\line_width=1
+axis_y\zero_line\color=#FAFAFA
+axis_colorbar_right\color=#FAFAFA
+axis_colorbar_right\draw_mode2=line+ticks+labels+axislabel
+axis_colorbar_right\line_width=1
+axis_colorbar_right\grid\color=#616161
+axis_colorbar_right\minor_tick\inside_length=2
+axis_colorbar_right\minor_tick\outside_length=2
+axis_colorbar_right\ticks\width=1
+axis_colorbar_right\zero_line\line_width=1
+axis_colorbar_right\zero_line\color=#FAFAFA
+axis_colorbar_top\color=#FAFAFA
+axis_colorbar_top\line_width=1
+axis_colorbar_top\grid\color=#616161
+axis_colorbar_top\minor_tick\inside_length=2
+axis_colorbar_top\minor_tick\outside_length=2
+axis_colorbar_top\ticks\width=1
+axis_colorbar_top\zero_line\line_width=1
+axis_colorbar_top\zero_line\color=#FAFAFA
+graphs\auto_styles\color0="#6DFF42,80%"
+graphs\auto_styles\color1="#FF3D00,80%"
+graphs\auto_styles\color2="#24C7FF,80%"
+graphs\auto_styles\color3="#FFEB3B,80%"
+graphs\auto_styles\color4="#FF9800,80%"
+graphs\auto_styles\color5="#9C27B0,80%"
+graphs\auto_styles\color6="#29B6F6,80%"
+graphs\auto_styles\color7="blue,80%"

fast/doc/fonts/UFL.txt

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+-------------------------------
+UBUNTU FONT LICENCE Version 1.0
+-------------------------------
+
+PREAMBLE
+This licence allows the licensed fonts to be used, studied, modified and
+redistributed freely. The fonts, including any derivative works, can be
+bundled, embedded, and redistributed provided the terms of this licence
+are met. The fonts and derivatives, however, cannot be released under
+any other licence. The requirement for fonts to remain under this
+licence does not require any document created using the fonts or their
+derivatives to be published under this licence, as long as the primary
+purpose of the document is not to be a vehicle for the distribution of
+the fonts.
+
+DEFINITIONS
+"Font Software" refers to the set of files released by the Copyright
+Holder(s) under this licence and clearly marked as such. This may
+include source files, build scripts and documentation.
+
+"Original Version" refers to the collection of Font Software components
+as received under this licence.
+
+"Modified Version" refers to any derivative made by adding to, deleting,
+or substituting -- in part or in whole -- any of the components of the
+Original Version, by changing formats or by porting the Font Software to
+a new environment.
+
+"Copyright Holder(s)" refers to all individuals and companies who have a
+copyright ownership of the Font Software.
+
+"Substantially Changed" refers to Modified Versions which can be easily
+identified as dissimilar to the Font Software by users of the Font
+Software comparing the Original Version with the Modified Version.
+
+To "Propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy. Propagation includes copying,
+distribution (with or without modification and with or without charging
+a redistribution fee), making available to the public, and in some
+countries other activities as well.
+
+PERMISSION & CONDITIONS
+This licence does not grant any rights under trademark law and all such
+rights are reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of the Font Software, to propagate the Font Software, subject to
+the below conditions:
+
+1) Each copy of the Font Software must contain the above copyright
+notice and this licence. These can be included either as stand-alone
+text files, human-readable headers or in the appropriate machine-
+readable metadata fields within text or binary files as long as those
+fields can be easily viewed by the user.
+
+2) The font name complies with the following:
+(a) The Original Version must retain its name, unmodified.
+(b) Modified Versions which are Substantially Changed must be renamed to
+avoid use of the name of the Original Version or similar names entirely.
+(c) Modified Versions which are not Substantially Changed must be
+renamed to both (i) retain the name of the Original Version and (ii) add
+additional naming elements to distinguish the Modified Version from the
+Original Version. The name of such Modified Versions must be the name of
+the Original Version, with "derivative X" where X represents the name of
+the new work, appended to that name.
+
+3) The name(s) of the Copyright Holder(s) and any contributor to the
+Font Software shall not be used to promote, endorse or advertise any
+Modified Version, except (i) as required by this licence, (ii) to
+acknowledge the contribution(s) of the Copyright Holder(s) or (iii) with
+their explicit written permission.
+
+4) The Font Software, modified or unmodified, in part or in whole, must
+be distributed entirely under this licence, and must not be distributed
+under any other licence. The requirement for fonts to remain under this
+licence does not affect any document created using the Font Software,
+except any version of the Font Software extracted from a document
+created using the Font Software may only be distributed under this
+licence.
+
+TERMINATION
+This licence becomes null and void if any of the above conditions are
+not met.
+
+DISCLAIMER
+THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF
+COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE
+COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM OTHER
+DEALINGS IN THE FONT SOFTWARE.

fast/entry_points.py

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+import subprocess
+import sys
+import os
+
+bin_path = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'bin'))
+
+def runUFFviewer():
+    subprocess.run([os.path.join(bin_path, 'UFFviewer')] + sys.argv[1:])
+
+def runSystemCheck():
+    subprocess.run([os.path.join(bin_path, 'systemCheck')] + sys.argv[1:])
+
+def runRunPipeline():
+    subprocess.run([os.path.join(bin_path, 'runPipeline')] + sys.argv[1:])