Merge pull request #9 from brandonjnelsonFDA/python

merge commit

Author: brandonjnelsonFDA

.gitignore

@@ -13,4 +13,3 @@ octave-workspace
 notebooks/data
 *.egg-info
 docs/build
-# Ignore Python bytecode and cache files

README.rst

@@ -48,8 +48,10 @@ If required versions of Matlab or Octave are not available on your system (see h
 
 .. code-block:: shell
 
-    git clone https://github.com/DIDSR/LCD_CT
-    cd LCD_CT
+        git clone https://github.com/DIDSR/LCD_CT
+        cd LCD_CT
+        conda env create --file environment.yml
+        conda activate LCD_CT
 
 2. *If neither Matlab or Octave are installed or do not meet the `version requirements`_, you can source `install.sh` to prepare a `conda <https://conda.io/projects/conda/en/latest/user-guide/install/index.html>`_ environment. Note: this can take about 10 minutes to complete.
 

build/lib/LCD/LCD.py

@@ -0,0 +1,20 @@
+"""
+Low Contrast Detectability (LCD)
+"""
+from pathlib import Path
+
+from oct2py import octave
+import pandas as pd
+
+def measure_LCD(sp_vol, sa_vol, sp_gt_vol, observers=None):
+    curdir = Path(__file__).parent.absolute()
+    # octave.cd('../../LCD_CT/src/LCD')
+    signal_present_array = sp_vol.transpose(1, 2, 0)
+    signal_absent_array = sa_vol.transpose(1, 2, 0)
+    print(curdir)
+    octave.pwd()
+    octave.addpath(curdir / 'classes')
+    octave.addpath(curdir / 'functions')
+    res = octave.measure_LCD(signal_present_array, signal_absent_array, sp_gt_vol)
+    res = {k: v.squeeze() for k, v in res.items()}
+    return pd.DataFrame(res)

environment.yml

@@ -0,0 +1,22 @@
+name: LCD_CT
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - octave
+  - cxx-compiler
+  - pandas
+  - tomli
+  - numpy
+  - oct2py
+  - pytest
+  - sphinx-tabs
+  - pandoc
+  - ipykernel
+  - pip
+  - pip:
+    - "git+https://github.com/DIDSR/pediatricIQphantoms"
+    - sphinxcontrib-svg2pdfconverter
+    - nbsphinx

install.sh

@@ -1,4 +1,5 @@
-conda create --name octave -y && conda activate octave
+conda create --name octave -y
+conda activate octave
 conda install -c conda-forge octave -y
 conda install -c conda-forge cxx-compiler -y