refactor code

ad12 · Oct 6, 2018 · 070b652 · 070b652
1 parent 037a11e
commit 070b652
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Showing 27 changed files with 746 additions and 562 deletions.
diff --git a/defaults.py b/defaults.py
@@ -1,3 +1,14 @@
-DEFAULT_BATCH_SIZE = 32
+# Default inference batch size - based on RAM of computer
+# for 16 GB RAM , recommend 16
+DEFAULT_BATCH_SIZE = 16
 
-FIX_VISUALIZATION_BOUNDS = True
+# Fix the bounds for the visualization colorbar based on the quantitative measure (T2, T1rho, etc)
+# if any value exceeds these bounds, automatically set this parameter to False
+FIX_VISUALIZATION_BOUNDS = True
+
+# The dilation rate we use for dilating any mask before registration
+DEFAULT_MASK_DIL_RATE = 8.0
+DEFAULT_MASK_DIL_THRESHOLD = 0.2
+
+# The R^2 fit threshold to include when estimating quantitative values
+DEFAULT_R2_THRESHOLD = 0.9
diff --git a/elastix_params/parameters-affine-interregister.txt b/elastix_params/parameters-affine-interregister.txt
@@ -0,0 +1,69 @@
+// *********************
+// * affine
+// *********************
+
+// *********************
+// * ImageTypes
+// *********************
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// *********************
+// * Components
+// *********************
+(FixedImagePyramid "FixedSmoothingImagePyramid")
+(MovingImagePyramid "MovingSmoothingImagePyramid")
+(Registration "MultiResolutionRegistration")
+(Interpolator "BSplineInterpolator")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Metric "AdvancedMattesMutualInformation")
+(BSplineInterpolationOrder 1)
+(Resampler "DefaultResampler")
+(Optimizer "AdaptiveStochasticGradientDescent")
+(Transform "AffineTransform")
+
+// *********************
+// * Mask settings
+// *********************
+(ErodeMask "false")
+(ErodeFixedMask "false")
+
+// *********************
+// * Optimizer settings
+// *********************
+(NumberOfResolutions 1)
+(MaximumNumberOfIterations 1000)
+(ASGDParameterEstimationMethod "Original")
+(AutomaticParameterEstimation "true")
+(AutomaticTransformInitialization "true")
+(AutomaticScalesEstimation "true")
+
+// *********************
+// * Transform settings
+// *********************
+(HowToCombineTransforms "Compose")
+
+// *********************
+// * Pyramid settings
+// *********************
+(NumberOfHistogramBins 32)
+
+
+// *********************
+// * Sampler parameters
+// *********************
+(NumberOfSpatialSamples 2000)
+(ImageSampler "RandomSparseMask")
+(CheckNumberOfSamples "true")
+(NewSamplesEveryIteration "true")
+(FinalBSplineInterpolationOrder 3)
+
+// *********************
+// * Output settings
+// *********************
+(DefaultPixelValue 0)
+(WriteTransformParametersEachIteration "false")
+(WriteResultImage  "true")
+(ResultImageFormat "nii.gz")
+(ResultImagePixelType "float")
diff --git a/elastix_params/parameters-rigid-interregister.txt b/elastix_params/parameters-rigid-interregister.txt
@@ -0,0 +1,69 @@
+// *********************
+// * rigid
+// *********************
+
+// *********************
+// * ImageTypes
+// *********************
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// *********************
+// * Components
+// *********************
+(FixedImagePyramid "FixedSmoothingImagePyramid")
+(MovingImagePyramid "MovingSmoothingImagePyramid")
+(Registration "MultiResolutionRegistration")
+(Interpolator "BSplineInterpolator")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Metric "AdvancedMattesMutualInformation")
+(BSplineInterpolationOrder 1)
+(Resampler "DefaultResampler")
+(Optimizer "AdaptiveStochasticGradientDescent")
+(Transform "EulerTransform")
+
+// *********************
+// * Mask settings
+// *********************
+(ErodeMask "false")
+(ErodeFixedMask "false")
+
+// *********************
+// * Optimizer settings
+// *********************
+(NumberOfResolutions 3)
+(MaximumNumberOfIterations 1000)
+(ASGDParameterEstimationMethod "Original")
+(AutomaticParameterEstimation "true")
+(AutomaticTransformInitialization "true")
+(AutomaticScalesEstimation "true")
+
+// *********************
+// * Transform settings
+// *********************
+(HowToCombineTransforms "Compose")
+
+// *********************
+// * Pyramid settings
+// *********************
+(NumberOfHistogramBins 32)
+
+
+// *********************
+// * Sampler parameters
+// *********************
+(NumberOfSpatialSamples 2000)
+(ImageSampler "RandomSparseMask")
+(CheckNumberOfSamples "true")
+(NewSamplesEveryIteration "true")
+(FinalBSplineInterpolationOrder 3)
+
+// *********************
+// * Output settings
+// *********************
+(DefaultPixelValue 0)
+(WriteTransformParametersEachIteration "false")
+(WriteResultImage  "true")
+(ResultImageFormat "nii.gz")
+(ResultImagePixelType "float")
diff --git a/environment.yml b/environment.yml
@@ -1,111 +1,111 @@
 name: tf
 channels:
-  - conda-forge
-  - defaults
+- conda-forge
+- defaults
 dependencies:
-  - boost=1.68.0=py36h3e44d54_0
-  - boost-cpp=1.68.0=h3a22d5f_0
-  - bzip2=1.0.6=1
-  - icu=58.2=hfc679d8_0
-  - blas=1.0=mkl
-  - ca-certificates=2018.03.07=0
-  - certifi=2018.8.24=py36_1
-  - cycler=0.10.0=py36hfc81398_0
-  - freetype=2.9.1=hb4e5f40_0
-  - intel-openmp=2019.0=118
-  - kiwisolver=1.0.1=py36h0a44026_0
-  - libcxx=4.0.1=h579ed51_0
-  - libcxxabi=4.0.1=hebd6815_0
-  - libedit=3.1.20170329=hb402a30_2
-  - libffi=3.2.1=h475c297_4
-  - libgfortran=3.0.1=h93005f0_2
-  - libopenblas=0.2.20=hdc02c5d_7
-  - libpng=1.6.34=he12f830_0
-  - matplotlib=3.0.0=py36h54f8f79_0
-  - mkl=2019.0=118
-  - mkl_fft=1.0.6=py36hb8a8100_0
-  - mkl_random=1.0.1=py36h5d10147_1
-  - ncurses=6.1=h0a44026_0
-  - numpy=1.15.2=py36h6a91979_0
-  - numpy-base=1.15.2=py36h8a80b8c_0
-  - openssl=1.0.2p=h1de35cc_0
-  - pip=10.0.1=py36_0
-  - pyparsing=2.2.0=py36_1
-  - python=3.6.6=hc167b69_0
-  - python-dateutil=2.7.3=py36_0
-  - pytz=2018.5=py36_0
-  - readline=7.0=hc1231fa_4
-  - setuptools=40.0.0=py36_0
-  - six=1.11.0=py36_1
-  - sqlite=3.24.0=ha441bb4_0
-  - tk=8.6.7=h35a86e2_3
-  - tornado=5.1=py36h1de35cc_0
-  - wheel=0.31.1=py36_0
-  - xz=5.2.4=h1de35cc_4
-  - zlib=1.2.11=hf3cbc9b_2
-  - pip:
-    - absl-py==0.4.0
-    - apipkg==1.5
-    - astor==0.7.1
-    - atomicwrites==1.2.1
-    - attrs==18.2.0
-    - bleach==1.5.0
-    - click==6.7
-    - configparser==3.5.0
-    - decorator==4.3.0
-    - deprecated==1.2.1
-    - dicom2nifti==2.0.3
-    - et-xmlfile==1.0.1
-    - execnet==1.5.0
-    - funcsigs==1.0.2
-    - future==0.16.0
-    - gast==0.2.0
-    - graphviz==0.9
-    - grpcio==1.14.1
-    - h5py==2.8.0
-    - html5lib==0.9999999
-    - isodate==0.6.0
-    - jdcal==1.4
-    - keras==2.1.6
-    - lxml==4.2.5
-    - markdown==2.6.11
-    - mock==2.0.0
-    - more-itertools==4.3.0
-    - mpmath==1.0.0
-    - natsort==5.3.3
-    - networkx==2.1
-    - nibabel==2.3.0
-    - nipy==0.4.2
-    - nipype==1.1.2
-    - opencv-python==3.4.2.17
-    - openpyxl==2.5.8
-    - packaging==17.1
-    - pandas==0.23.4
-    - pbr==4.2.0
-    - pillow==5.2.0
-    - pluggy==0.7.1
-    - protobuf==3.6.1
-    - prov==1.5.0
-    - psutil==5.4.7
-    - py==1.6.0
-    - pydicom==1.1.0
-    - pydot==1.2.4
-    - pydotplus==2.0.2
-    - pytest==3.8.0
-    - pytest-forked==0.2
-    - pytest-xdist==1.23.0
-    - pywavelets==0.5.2
-    - pyyaml==3.13
-    - rdflib==4.2.2
-    - scikit-image==0.13.1
-    - scipy==1.1.0
-    - simpleitk==1.1.0
-    - simplejson==3.16.0
-    - sympy==1.3
-    - tensorboard==1.8.0
-    - tensorflow==1.8.0
-    - termcolor==1.1.0
-    - traits==4.6.0
-    - werkzeug==0.14.1
-    - wrapt==1.10.11
+- boost=1.68.0=py36h3e44d54_0
+- boost-cpp=1.68.0=h3a22d5f_0
+- bzip2=1.0.6=1
+- icu=58.2=hfc679d8_0
+- blas=1.0=mkl
+- ca-certificates=2018.03.07=0
+- certifi=2018.8.24=py36_1
+- cycler=0.10.0=py36hfc81398_0
+- freetype=2.9.1=hb4e5f40_0
+- intel-openmp=2019.0=118
+- kiwisolver=1.0.1=py36h0a44026_0
+- libcxx=4.0.1=h579ed51_0
+- libcxxabi=4.0.1=hebd6815_0
+- libedit=3.1.20170329=hb402a30_2
+- libffi=3.2.1=h475c297_4
+- libgfortran=3.0.1=h93005f0_2
+- libopenblas=0.2.20=hdc02c5d_7
+- libpng=1.6.34=he12f830_0
+- matplotlib=3.0.0=py36h54f8f79_0
+- mkl=2019.0=118
+- mkl_fft=1.0.6=py36hb8a8100_0
+- mkl_random=1.0.1=py36h5d10147_1
+- ncurses=6.1=h0a44026_0
+- numpy=1.15.2=py36h6a91979_0
+- numpy-base=1.15.2=py36h8a80b8c_0
+- openssl=1.0.2p=h1de35cc_0
+- pip=10.0.1=py36_0
+- pyparsing=2.2.0=py36_1
+- python=3.6.6=hc167b69_0
+- python-dateutil=2.7.3=py36_0
+- pytz=2018.5=py36_0
+- readline=7.0=hc1231fa_4
+- setuptools=40.0.0=py36_0
+- six=1.11.0=py36_1
+- sqlite=3.24.0=ha441bb4_0
+- tk=8.6.7=h35a86e2_3
+- tornado=5.1=py36h1de35cc_0
+- wheel=0.31.1=py36_0
+- xz=5.2.4=h1de35cc_4
+- zlib=1.2.11=hf3cbc9b_2
+- pip:
+  - absl-py==0.4.0
+  - apipkg==1.5
+  - astor==0.7.1
+  - atomicwrites==1.2.1
+  - attrs==18.2.0
+  - bleach==1.5.0
+  - click==6.7
+  - configparser==3.5.0
+  - decorator==4.3.0
+  - deprecated==1.2.1
+  - dicom2nifti==2.0.3
+  - et-xmlfile==1.0.1
+  - execnet==1.5.0
+  - funcsigs==1.0.2
+  - future==0.16.0
+  - gast==0.2.0
+  - graphviz==0.9
+  - grpcio==1.14.1
+  - h5py==2.8.0
+  - html5lib==0.9999999
+  - isodate==0.6.0
+  - jdcal==1.4
+  - keras==2.1.6
+  - lxml==4.2.5
+  - markdown==2.6.11
+  - mock==2.0.0
+  - more-itertools==4.3.0
+  - mpmath==1.0.0
+  - natsort==5.3.3
+  - networkx==2.1
+  - nibabel==2.3.0
+  - nipy==0.4.2
+  - nipype==1.1.2
+  - opencv-python==3.4.2.17
+  - openpyxl==2.5.8
+  - packaging==17.1
+  - pandas==0.23.4
+  - pbr==4.2.0
+  - pillow==5.2.0
+  - pluggy==0.7.1
+  - protobuf==3.6.1
+  - prov==1.5.0
+  - psutil==5.4.7
+  - py==1.6.0
+  - pydicom==1.1.0
+  - pydot==1.2.4
+  - pydotplus==2.0.2
+  - pytest==3.8.0
+  - pytest-forked==0.2
+  - pytest-xdist==1.23.0
+  - pywavelets==0.5.2
+  - pyyaml==3.13
+  - rdflib==4.2.2
+  - scikit-image==0.13.1
+  - scipy==1.1.0
+  - simpleitk==1.1.0
+  - simplejson==3.16.0
+  - sympy==1.3
+  - tensorboard==1.8.0
+  - tensorflow==1.8.0
+  - termcolor==1.1.0
+  - traits==4.6.0
+  - werkzeug==0.14.1
+  - wrapt==1.10.11
 prefix: /Users/arjundesai/anaconda3/envs/tf
diff --git a/file_constants.py b/file_constants.py
@@ -11,14 +11,19 @@
 ELASTIX_BSPLINE_PARAMS_FILE = os.path.join(__PATH_TO_ELASTIX_FOLDER__, 'parameters-bspline.txt')
 ELASTIX_RIGID_PARAMS_FILE = os.path.join(__PATH_TO_ELASTIX_FOLDER__, 'parameters-rigid.txt')
 
+ELASTIX_AFFINE_INTERREGISTER_PARAMS_FILE = os.path.join(__PATH_TO_ELASTIX_FOLDER__,
+                                                        'parameters-affine-interregister.txt')
+ELASTIX_RIGID_INTERREGISTER_PARAMS_FILE = os.path.join(__PATH_TO_ELASTIX_FOLDER__,
+                                                       'parameters-rigid-intraregister.txt')
 
 # Temporary file path
 TEMP_FOLDER_PATH = os.path.join(__DIR__, 'temp')
 
 # TODO: nipype logging
 NIPYPE_LOGGING = 'none'
 
+
 def set_debug():
     global DEBUG, NIPYPE_LOGGING
-    DEBUG=1
-    NIPYPE_LOGGING = 'stream'
+    DEBUG = 1
+    NIPYPE_LOGGING = 'stream'
diff --git a/med_objects/__init__.py b/med_objects/__init__.py