WIP: Mesh saving and Rendering

BrownBiomechanics · Apr 17, 2023 · ef21f0f · ef21f0f
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diff --git a/CMakeLists.txt.user b/CMakeLists.txt.user
diff --git a/CMakeSettings.json b/CMakeSettings.json
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+{
+    "configurations": [
+        {
+            "name": "x64-Debug",
+            "generator": "Ninja",
+            "configurationType": "Debug",
+            "inheritEnvironments": [ "msvc_x64" ],
+            "buildRoot": "${projectDir}\\out\\build\\${name}",
+            "installRoot": "${projectDir}\\out\\install\\${name}",
+            "cmakeCommandArgs": "-DQt5_DIR=\"C:/Qt/5.15.2/msvc2019_64/lib/cmake/Qt5\" -DAutoscoper_RENDERING_BACKEND=\"OpenCL\"",
+            "buildCommandArgs": "",
+            "ctestCommandArgs": ""
+        }
+    ]
+}
diff --git a/Documentation/_build/.buildinfo b/Documentation/_build/.buildinfo
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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 981409d9891d278a66a3db0b507032d5
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/Documentation/_build/.doctrees/environment.pickle b/Documentation/_build/.doctrees/environment.pickle
diff --git a/Documentation/_build/.doctrees/index.doctree b/Documentation/_build/.doctrees/index.doctree
diff --git a/Documentation/_build/.doctrees/socket-control-libraries/index.doctree b/Documentation/_build/.doctrees/socket-control-libraries/index.doctree
diff --git a/Documentation/_build/.doctrees/socket-control-libraries/pyautoscoper.doctree b/Documentation/_build/.doctrees/socket-control-libraries/pyautoscoper.doctree
diff --git a/Documentation/_build/.doctrees/test.doctree b/Documentation/_build/.doctrees/test.doctree
diff --git a/Documentation/_build/404.html b/Documentation/_build/404.html
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diff --git a/Documentation/_build/_sources/index.md.txt b/Documentation/_build/_sources/index.md.txt
@@ -0,0 +1,25 @@
+<!--- Autoscoper documentation master file, created by
+   sphinx-quickstart on Mon Apr 10 14:29:37 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive. -->
+
+# Welcome to Autoscoper's documentation!
+
+Autoscoper enables the 3D tracking of structures within multiple imaging modalities including single, bi-, and multi-plane videoradiography, sequential CT volume images, 4DCT image volumes sets, and MRI volume sets.
+
+Autoscoper has been used for tracking the shoulder, spine, wrist, hip, knee, and ankle joints.
+
+```{toctree}
+:maxdepth: 2
+:caption: Contents:
+
+socket-control-libraries/index.md
+```
+
+
+
+# Indices and tables
+
+* {ref}`genindex`
+* {ref}`modindex`
+* {ref}`search`
diff --git a/Documentation/_build/_sources/socket-control-libraries/index.md.txt b/Documentation/_build/_sources/socket-control-libraries/index.md.txt
@@ -0,0 +1,6 @@
+# Autoscoper Socket Control Libraries
+
+```{toctree}
+:maxdepth: 2
+pyautoscoper.md
+```
diff --git a/Documentation/_build/_sources/socket-control-libraries/pyautoscoper.md.txt b/Documentation/_build/_sources/socket-control-libraries/pyautoscoper.md.txt
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+# PyAutoscoper
+
+## Overview
+
+PyAutoscoper is a Python library for controlling Autoscoper via a TCP socket connection. It provides a simple interface for sending commands and receiving responses from Autoscoper.
+
+## Installation
+
+Install the latest version of PyAutoscoper from PyPI using pip:
+
+```bash
+$ pip install pyautoscoper
+```
+
+## Usage
+
+### Connecting to Autoscoper
+
+The AutoscoperConnection class can be created with two optional arguments:
+* `address`: The IP address of the Autoscoper server. Default is `127.0.0.1` (localhost).
+* `verbose`: If True, the methods will print out information about the connection. Default is False.
+
+Ensure that Autoscoper is running, the class will attempt to connect to Autoscoper upon instantiation. If the connection is successful, the is_connected method will return True.
+
+```{literalinclude} ../../scripts/python/examples/pyautoscoper-examples.py
+:language: python
+:caption: Connecting to Autoscoper
+:start-after: "[Example 1 - Start]"
+:end-before: "[Example 1 - End]"
+```
+
+### Loading a trial
+
+This example will load the trial configuration file `trial_config.cfg` and the filter settings file `filter_settings.vie` for both cameras.
+
+The loadTrial method takes one argument:
+* `trial_config`: The path to the trial configuration file.
+
+The loadFilter method takes two arguments:
+* `camera`: The camera number (0-indexed).
+* `f`ilter_file`: The path to the filter settings file.
+
+```{literalinclude} ../../scripts/python/examples/pyautoscoper-examples.py
+:language: python
+:caption: Loading a trial
+:start-after: "[Example 2 - Start]"
+:end-before: "[Example 2 - End]"
+```
+
+### Loading and Saving Tracking Data
+
+This example will load the tracking data file `tracking_data.tra` and save it as `tracking_data_out.tra`.
+
+NOTE: A trial must be loaded before loading tracking data.
+
+The loadTrackingData method takes at least two arguments:
+* `volume`: The volume index (0-indexed).
+* `tracking_data`: The path to the tracking data file.
+* `is_matrix`: If True, the tracking data will be loaded as a 4 by 4 matrix. If False, the tracking data will be loaded in xyz roll pitch yaw format. Defaults to True.
+* `is_rows`: If True, the tracking data will be loaded as rows. If False, the tracking data will be loaded as columns. Defaults to True.
+* `is_with_commas`: If True, the tracking data will be loaded with commas. If False, the tracking data will be loaded with spaces. Defaults to True.
+* `is_cm`: If True, the tracking data will be loaded in cm. If False, the tracking data will be loaded in mm. Defaults to False.
+* `is_rad`: If True, the tracking data will be loaded in radians. If False, the tracking data will be loaded in degrees. Defaults to False.
+* `interpolate`: If True, the tracking data will be interpolated with the spline method. If False, the tracking data will not be interpolated (NaN values). Defaults to False.
+
+The saveTrackingData method takes at least two arguments:
+* `volume`: The volume index (0-indexed).
+* `tracking_data`: The path to the tracking data file.
+* `save_as_matrix`: If True, the tracking data will be saved as a 4 by 4 matrix. If False, the tracking data will be saved in xyz roll pitch yaw format. Defaults to True.
+* `save_as_rows`: If True, the tracking data will be saved as rows. If False, the tracking data will be saved as columns. Defaults to True.
+* `save_with_commas`: If True, the tracking data will be saved with commas. If False, the tracking data will be saved with spaces. Defaults to True.
+* `convert_to_cm`: If True, the tracking data will be saved in cm. If False, the tracking data will be saved in mm. Defaults to False.
+* `convert_to_rad`: If True, the tracking data will be saved in radians. If False, the tracking data will be saved in degrees. Defaults to False.
+* `interpolate`: If True, the tracking data will be interpolated with the spline method. If False, the tracking data will not be interpolated (NaN values). Defaults to False.
+
+```{literalinclude} ../../scripts/python/examples/pyautoscoper-examples.py
+:language: python
+:caption: Loading and Saving Tracking Data
+:start-after: "[Example 3 - Start]"
+:end-before: "[Example 3 - End]"
+```
+
+### Changing the Current Frame and Pose
+
+This example will change the pose on multiple frames.
+
+NOTE: A trial must be loaded before changing the current frame and pose.
+
+The setPose method takes three arguments:
+* `volume`: The volume index (0-indexed).
+* `frame`: The frame index (0-indexed).
+* `pose`: The pose of the volume in the form of an array of 6 floats. Array order is [x, y, z, roll, pitch, yaw].
+
+The getPose method takes two arguments:
+* `volume`: The volume index (0-indexed).
+* `frame`: The frame index (0-indexed).
+
+The setFrame method takes one argument:
+* `frame`: The frame index (0-indexed).
+
+```{literalinclude} ../../scripts/python/examples/pyautoscoper-examples.py
+:language: python
+:caption: Changing the Current Frame and Pose
+:start-after: "[Example 4 - Start]"
+:end-before: "[Example 4 - End]"
+```
+
+### Optimizations
+
+There are two methods for optimizing the tracking data:
+* `optimizeFrame`: Optimizes the tracking data for a single frame.
+* `trackingDialog`: Automatically optimizes the tracking data for all given frames.
+
+The optimizeFrame method takes ten arguments:
+* `volume`: The volume index (0-indexed).
+* `frame`: The frame index (0-indexed).
+* `repeats`: The number of times to repeat the optimization.
+* `max_itr`: The maximum number of iterations to run the optimization.
+* `min_lim`: The minimum limit for the PSO movement.
+* `max_lim`: The maximum limit for the PSO movement.
+* `max_stall_itr`: The maximum number of iterations to stall the optimization.
+* `dframe`: The amount of frames to skip backwards for the intial guess.
+* `opt_method`: The optimization method to use, 0 for Particle Swarm, 1 for Downhill Simplex.
+* `cf_model`: The cost function to use, 0 for NCC (Bone Models), 1 for Sum of Absolute Differences (Implant Models)
+
+```{literalinclude} ../../scripts/python/examples/pyautoscoper-examples.py
+:language: python
+:caption: Optimizing a single frame
+:start-after: "[Example 5 - Start]"
+:end-before: "[Example 5 - End]"
+```
+
+The trackingDialog method takes at least three arguments:
+* `volume`: The volume index (0-indexed).
+* `start_frame`: The starting frame index (0-indexed).
+* `end_frame`: The ending frame index (0-indexed).
+* `frame_skip`: The number of frames to skip between each optimization. Defaults to 1.
+* `repeats`: The number of times to repeat the optimization. Defaults to 1.
+* `max_itr`: The maximum number of iterations to run the optimization. Defaults to 1000.
+* `min_lim`: The minimum limit for the PSO movement. Defaults to -3.0.
+* `max_lim`: The maximum limit for the PSO movement. Defaults to 3.0.
+* `max_stall_itr`: The maximum number of iterations to stall the optimization. Defaults to 25.
+* `opt_method`: The optimization method to use, 0 for Particle Swarm, 1 for Downhill Simplex. Defaults to 0.
+* `cf_model`: The cost function to use, 0 for NCC (Bone Models), 1 for Sum of Absolute Differences (Implant Models). Defaults to 0.
+
+```{literalinclude} ../../scripts/python/examples/pyautoscoper-examples.py
+:language: python
+:caption: Optimizing multiple frames
+:start-after: "[Example 5.1 - Start]"
+:end-before: "[Example 5.1 - End]"
+```
+
+### Putting it all together
+
+We can put all of the above examples together to create a script that will load a trial, load tracking data, optimize the tracking data, and save the tracking data.
+
+```{literalinclude} ../../scripts/python/examples/pyautoscoper-examples.py
+:language: python
+:caption: Putting it all together
+:start-after: "[Example 6 - Start]"
+:end-before: "[Example 6 - End]"
+```
+
+### Launching Autoscoper from Python
+
+It may be useful to launch Autoscoper from Python. This can be done by using the subprocess module.
+
+```{literalinclude} ../../scripts/python/examples/pyautoscoper-examples.py
+:language: python
+:caption: Launching Autoscoper from Python
+:start-after: "[Example 7 - Start]"
+:end-before: "[Example 7 - End]"
+```
+
+## Class Reference
+
+```{eval-rst}
+.. automodule:: PyAutoscoper.connect
+   :members:
+   :undoc-members:
+   :show-inheritance:
+```
+
diff --git a/Documentation/_build/_sources/test.md.txt b/Documentation/_build/_sources/test.md.txt
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+# This is a test of Markdown with Sphinx