+
+ {% endblock %}
+
+
+
diff --git a/myapp/templates/errors/404.html b/myapp/templates/errors/404.html
new file mode 100644
index 0000000..0b0b68e
--- /dev/null
+++ b/myapp/templates/errors/404.html
@@ -0,0 +1,20 @@
+
+
+
+
+
+
+
+ Oops looks like you don't have access to this page !
+
+
+ {% endblock %}
+
+
+
diff --git a/myapp/templates/errors/500.html b/myapp/templates/errors/500.html
new file mode 100644
index 0000000..848ddf5
--- /dev/null
+++ b/myapp/templates/errors/500.html
@@ -0,0 +1,20 @@
+
+
+
+
+
+
+
+ Oops this page does not exist !
+
+
+ {% endblock %}
+
+
+
diff --git a/myapp/templates/maintenance.html b/myapp/templates/maintenance.html
new file mode 100644
index 0000000..ad8b1ed
--- /dev/null
+++ b/myapp/templates/maintenance.html
@@ -0,0 +1,20 @@
+
+
+
+
+
+
+
+ Oops an error happened !
+
+
+ {% endblock %}
+
+
+
\ No newline at end of file
diff --git a/myapp/templates/patient.html b/myapp/templates/patient.html
new file mode 100644
index 0000000..a257d8f
--- /dev/null
+++ b/myapp/templates/patient.html
@@ -0,0 +1,18 @@
+@extends 'base.html'
+
+
+@block content
+
+
+
+@endblock
+
+
diff --git a/myapp/templates/welcome.html b/myapp/templates/welcome.html
new file mode 100644
index 0000000..837ae2a
--- /dev/null
+++ b/myapp/templates/welcome.html
@@ -0,0 +1,34 @@
+{% extends "base.html" %}
+{% block title %}Welcome on Masonite 4{% endblock %}
+
+{% block content %}
+Sorry, this site is currently down for maintenance.
+
+ 
+
+{% endblock %}
diff --git a/myapp/tests/TestCase.py b/myapp/tests/TestCase.py
new file mode 100644
index 0000000..f642e7f
--- /dev/null
+++ b/myapp/tests/TestCase.py
@@ -0,0 +1,6 @@
+from masonite.tests import TestCase
+
+
+class TestCase(TestCase):
+ def setUp(self):
+ super().setUp()
diff --git a/myapp/tests/__init__.py b/myapp/tests/__init__.py
new file mode 100644
index 0000000..975feaf
--- /dev/null
+++ b/myapp/tests/__init__.py
@@ -0,0 +1 @@
+from .TestCase import TestCase
diff --git a/myapp/tests/unit/test_basic_testcase.py b/myapp/tests/unit/test_basic_testcase.py
new file mode 100644
index 0000000..1025831
--- /dev/null
+++ b/myapp/tests/unit/test_basic_testcase.py
@@ -0,0 +1,6 @@
+from tests import TestCase
+
+
+class BasicTestCase(TestCase):
+ def test_basic_assertion(self):
+ self.assertTrue(True)
diff --git a/myapp/webpack.mix.js b/myapp/webpack.mix.js
new file mode 100644
index 0000000..677967c
--- /dev/null
+++ b/myapp/webpack.mix.js
@@ -0,0 +1,26 @@
+/* Mix provides a clean, fluent API for defining some Webpack build steps for your Masonite
+applications. By default, we are compiling the CSS file for the application as well as
+bundling up all the JS files. */
+const mix = require('laravel-mix')
+const path = require('path')
+
+
+mix.js('resources/js/app.js', 'storage/compiled/js')
+ .postCss('resources/css/app.css', 'storage/compiled/css', [
+ //
+ ])
+
+// ensure root directory of mix is project root
+mix.setPublicPath(".")
+
+// add an alias to js code
+mix.alias({
+ "@": path.resolve("resources/js/"),
+})
+
+// add version hash in production
+if (mix.inProduction()) {
+ mix.version()
+}
+// Disable compilation success notification
+mix.disableSuccessNotifications()
diff --git a/myapp/wsgi.py b/myapp/wsgi.py
new file mode 100644
index 0000000..a409dfd
--- /dev/null
+++ b/myapp/wsgi.py
@@ -0,0 +1,14 @@
+from masonite.foundation import Application, Kernel
+from masonite.utils.location import base_path
+from masonite.configuration import config
+
+from Kernel import Kernel as ApplicationKernel
+
+"""Start The Application Instance."""
+application = Application(base_path())
+
+"""Now Bind important providers needed to make the framework work."""
+application.register_providers(Kernel, ApplicationKernel)
+
+"""Now Bind important application specific providers needed to make the application work."""
+application.add_providers(*config("providers.providers"))
diff --git a/old/1-move.py b/old/1-move.py
new file mode 100755
index 0000000..ca61768
--- /dev/null
+++ b/old/1-move.py
@@ -0,0 +1,189 @@
+#!/usr/bin/env python3
+
+import os
+import sys
+import time
+
+from pydicom.dataset import Dataset
+
+from pynetdicom import AE, evt, StoragePresentationContexts, debug_logger
+from pynetdicom.sop_class import (
+ PatientRootQueryRetrieveInformationModelFind,
+ PatientRootQueryRetrieveInformationModelMove,
+ StudyRootQueryRetrieveInformationModelMove,
+ PatientStudyOnlyQueryRetrieveInformationModelMove,
+)
+
+# debug_logger()
+
+Series = {}
+
+dcm_dir = '/nn'
+
+def handle_store(event):
+# print(event)
+ """Handle a C-STORE request event."""
+ ds = event.dataset
+ ds.file_meta = event.file_meta
+
+# print(ds.SeriesInstanceUID)
+
+ if ds.SeriesInstanceUID in Series:
+ s = Series[ds.SeriesInstanceUID]
+ else:
+ number = len(Series)
+ series_dir = os.path.join(dcm_dir, ds.PatientID, ds.StudyInstanceUID, ds.SeriesInstanceUID, str(number))
+ series_dir = os.path.join(dcm_dir, ds.PatientID, ds.StudyDate, ds.Modality, str(number))
+ series_dir = os.path.join(dcm_dir, ds.PatientID, ds.StudyDate, ds.Modality, hex(number)[2:])
+ s = {
+ 'PatientID': ds.PatientID,
+ 'StudyInstanceUID': ds.StudyInstanceUID,
+ 'SeriesInstanceUID': ds.SeriesInstanceUID,
+
+ 'Modality': ds.Modality,
+ 'SeriesDescription': ds.SeriesDescription,
+
+ 'path': series_dir,
+ 'number': number,
+ }
+ # print(s)
+ print(s['path'], s['SeriesDescription'])
+ Series[ds.SeriesInstanceUID] = s
+
+ os.makedirs(s['path'], exist_ok=True)
+
+ filename = os.path.join(s['path'], ds.SOPInstanceUID)
+
+ # Save the dataset using the SOP Instance UID as the filename
+ ds.save_as(filename, write_like_original=False)
+
+ # Return a 'Success' status
+ return 0x0000
+
+# Search in nested Python dict
+def gen_dict_extract(key, var):
+ if hasattr(var,'items'):
+ for k, v in var.items():
+ if k == key:
+ yield v
+ if isinstance(v, dict):
+ for result in gen_dict_extract(key, v):
+ yield result
+ elif isinstance(v, list):
+ for d in v:
+ for result in gen_dict_extract(key, d):
+ yield result
+
+
+def FindElement(identifier, element):
+ e = None
+ for v in gen_dict_extract(element, identifier.to_json_dict()):
+ e = v['Value'][0]
+ return e
+
+def QueryDCM(PatientID):
+
+ handlers = [
+ (evt.EVT_C_STORE, handle_store),
+ ]
+
+# debug_logger()
+
+ StudyInstanceUID_LIST = []
+
+ ae = AE()
+ ae.add_requested_context(PatientRootQueryRetrieveInformationModelFind)
+ assoc = ae.associate("192.168.10.56", 104,
+ ae_title = 'IQWEBX',
+ )
+ ds = Dataset()
+ ds.QueryRetrieveLevel = 'PATIENT'
+ ds.PatientID = PatientID
+ responses = assoc.send_c_find(ds, PatientRootQueryRetrieveInformationModelFind)
+# print(responses)
+ for (status, identifier) in responses:
+# print(status, identifier)
+ if status:
+ print('C-FIND query status: 0x{0:04X}'.format(status.Status))
+ else:
+ print('Connection timed out, was aborted or received invalid response')
+
+ if identifier:
+ StudyInstanceUID = FindElement(identifier, '0020000D')
+ print(StudyInstanceUID)
+ StudyInstanceUID_LIST.append(StudyInstanceUID)
+ assoc.release()
+ print(StudyInstanceUID_LIST)
+
+
+
+ # Initialise the Application Entity
+ ae = AE()
+ # Add a requested presentation context
+ ae.add_requested_context(PatientRootQueryRetrieveInformationModelMove)
+
+ # Add the Storage SCP's supported presentation contexts
+ ae.supported_contexts = StoragePresentationContexts
+
+ # Start our Storage SCP in non-blocking mode, listening on port 11120
+ ae.ae_title = 'OUR_STORE_SCP'
+ # scp = ae.start_server(("127.0.0.1", 11120), block=False, evt_handlers=handlers)
+ scp = ae.start_server(("0.0.0.0", 11120), block=False, evt_handlers=handlers)
+
+ for StudyInstanceUID in StudyInstanceUID_LIST:
+
+ # Create out identifier (query) dataset
+ ds = Dataset()
+ # ds.QueryRetrieveLevel = 'PATIENT'
+ # ds.PatientID = PatientID
+ ds.QueryRetrieveLevel = 'STUDY'
+ ds.StudyInstanceUID = StudyInstanceUID
+
+
+ # Associate with peer AE at IP 127.0.0.1 and port 11112
+ # assoc = ae.associate("127.0.0.1", 11112)
+ assoc = ae.associate("192.168.10.56", 104,
+ ae_title = 'IQWEBX',
+ )
+
+ if assoc.is_established:
+
+ # Use the C-MOVE service to send the identifier
+ responses = assoc.send_c_move(ds, 'OUR_STORE_SCP', PatientRootQueryRetrieveInformationModelMove)
+
+ # print(responses)
+ for (status, identifier) in responses:
+# print(status, identifier)
+ if status:
+ print('C-MOVE query status: 0x{0:04x}'.format(status.Status))
+ else:
+ print('Connection timed out, was aborted or received invalid response')
+
+ # Release the association
+ assoc.release()
+ else:
+ print('Association rejected, aborted or never connected')
+
+ # Stop our Storage SCP
+ scp.shutdown()
+
+
+def main():
+ if len(sys.argv) < 2:
+ print('Usage:', sys.argv[0], 'PatientID')
+ sys.exit()
+ print('hello')
+ print(sys.argv[0])
+ print(sys.argv[1])
+
+ start = time.time()
+ QueryDCM(sys.argv[1])
+ end = time.time()
+ print(end - start, 'seconds')
+
+ # for k, v in Series.items():
+ # print(v['number'], v['Modality'], v['SeriesDescription'], v['path'])
+ # print(v['path'], v['SeriesDescription'])
+
+if __name__ == '__main__':
+ main()
diff --git a/3-send.py b/old/3-send.py
similarity index 100%
rename from 3-send.py
rename to old/3-send.py
diff --git a/itk_elastix.py b/old/itk_elastix.py
similarity index 100%
rename from itk_elastix.py
rename to old/itk_elastix.py
diff --git a/pxrjso6b.mat b/pxrjso6b.mat
new file mode 100644
index 0000000..ebe919e
Binary files /dev/null and b/pxrjso6b.mat differ
diff --git a/razmtoz2.mat b/razmtoz2.mat
new file mode 100644
index 0000000..992d9c6
Binary files /dev/null and b/razmtoz2.mat differ
diff --git a/registration/__init__.py b/registration/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/registration/ants_reg.py b/registration/ants_reg.py
new file mode 100644
index 0000000..dbc75fa
--- /dev/null
+++ b/registration/ants_reg.py
@@ -0,0 +1,82 @@
+from pprint import pprint
+
+import os
+import tempfile
+
+from skimage.metrics import normalized_mutual_information
+
+import ants
+
+class ants_reg:
+
+ def register_aux(self, fi, mv):
+ mytx = ants.registration(fixed=fi, moving=mv, type_of_transform = 'Rigid',
+ # verbose=True,
+ )
+
+# print(mytx['fwdtransforms'][0])
+ fwdtransforms = ants.read_transform(mytx['fwdtransforms'][0])
+
+ m1 = normalized_mutual_information(fi.numpy(), mytx['warpedmovout'].numpy())
+ m2 = normalized_mutual_information(mv.numpy(), mytx['warpedfixout'].numpy())
+
+
+ print(m1, m2)
+
+ return {
+ 'fwdtransforms': fwdtransforms,
+ 'invtransforms': fwdtransforms.invert(),
+ 'warpedfixout': mytx['warpedfixout'],
+ 'warpedmovout': mytx['warpedmovout'],
+ 'metrics': max(m1, m2)
+ }
+
+ def __init__(self, fi, mv, debug=False):
+ fixed_image = ants.image_read(fi, dimension=3)
+ moving_image = ants.image_read(mv, dimension=3)
+ r1 = self.register_aux(fixed_image, moving_image)
+ r2 = self.register_aux(moving_image, fixed_image)
+
+
+ if r1['metrics'] > r2['metrics']:
+ self.res = r1
+ else:
+ self.res = dict(r2)
+ self.res.update({
+ 'fwdtransforms': r2['invtransforms'],
+ 'invtransforms': r2['fwdtransforms'],
+ 'warpedfixout': r2['warpedmovout'],
+ 'warpedmovout': r2['warpedfixout'],
+ })
+ self.res.update({
+ 'fix': fixed_image,
+ 'mov': moving_image,
+ })
+
+
+ if debug:
+ pprint(self.res)
+ ants.image_write(fixed_image, '0fixed.nii.gz')
+ ants.image_write(moving_image, '0moving.nii.gz')
+ ants.image_write(r1['warpedfixout'], '0mf1.nii.gz')
+ ants.image_write(r1['warpedmovout'], '0fm1.nii.gz')
+ ants.image_write(r2['warpedmovout'], '0mf2.nii.gz')
+ ants.image_write(r2['warpedfixout'], '0fm2.nii.gz')
+
+ def get_metrics(self):
+ return self.res['metrics']
+
+ def transform(self, moving, output_filename, is_label=False):
+ transform1 = next(tempfile._get_candidate_names())+'.mat'
+ # print(transform1)
+ ants.write_transform(self.res['fwdtransforms'], transform1)
+ mi = ants.image_read(moving, dimension=3)
+ if is_label:
+ transformed = ants.apply_transforms(self.res['fix'], mi,
+ transformlist=[transform1], interpolator='genericLabel').astype('uint8')
+ else:
+ transformed = ants.apply_transforms(self.res['fix'], mi,
+ transformlist=[transform1])
+ # print(transformed)
+ ants.image_write(transformed, output_filename)
+ os.remove(transform1)
\ No newline at end of file
diff --git a/registration/best_reg.py b/registration/best_reg.py
new file mode 100644
index 0000000..c2e9459
--- /dev/null
+++ b/registration/best_reg.py
@@ -0,0 +1,76 @@
+import multiprocessing
+import os
+import shutil
+import tempfile
+import time
+
+from .ants_reg import ants_reg
+from .elastix_reg import elastix_reg
+
+Q = multiprocessing.Queue()
+
+def registration(method, fix, mov_image, mov_label):
+ start = time.time()
+
+ transformed = next(tempfile._get_candidate_names())+'.nii.gz'
+ r = method(fix, mov_image)
+ r.transform(mov_label, transformed, is_label=False)
+ r.transform(mov_label, transformed, is_label=True)
+
+ end = time.time()
+
+ res = {
+ 'name': r.__class__.__name__,
+ 'metrics': r.get_metrics(),
+ 'transformed': transformed,
+ 'time': end - start,
+ }
+
+ Q. put(res)
+ return r.get_metrics()
+
+
+def dump_queue(q):
+ q.put(None)
+ return list(iter(lambda : q.get(timeout=0.00001), None))
+
+
+def reg_transform(fix, mov_image, mov_label, out_label):
+ regs = [ants_reg, elastix_reg]
+
+ inputs = [(r, fix, mov_image, mov_label) for r in regs]
+ pool = multiprocessing.Pool(4)
+ # print(inputs)
+ pool_outputs = pool.starmap(registration, inputs)
+ pool.close()
+
+ print(pool_outputs)
+ rlist = dump_queue(Q)
+# print(rlist)
+ rlist2 = sorted(rlist, key=lambda r: -r['metrics'])
+ print(rlist2)
+
+ shutil.copy(rlist2[0]['transformed'], out_label)
+
+ for r in rlist2:
+ os.remove(r['transformed'])
+
+
+fi = '/nn/2896833/20220506/nii/b_C+MAR_20220506155936_301.nii.gz'
+mv_img = '/nn/2896833/20220506/nii/9_3D_fl3d_mt_FS_+_c_MPR_Tra_20220506142416_15.nii.gz'
+mv_lab = '/nn/2896833/20220506/output/9_3D_fl3d_mt_FS_+_c_MPR_Tra_20220506142416.nii.gz'
+
+
+if __name__ == '__main__':
+ reg_transform(fi, mv_img, mv_lab, 'tmp.nii.gz')
+
+ # regs = [ants_reg, elastix_reg]
+
+ # inputs = [(r, fi, mv) for r in regs]
+ # pool = multiprocessing.Pool(4)
+ # # print(inputs)
+ # pool_outputs = pool.starmap(registration, inputs)
+ # pool.close()
+
+ # print(pool_outputs)
+ # print(dump_queue(Q))
diff --git a/registration/elastix_reg.py b/registration/elastix_reg.py
new file mode 100644
index 0000000..29d33d2
--- /dev/null
+++ b/registration/elastix_reg.py
@@ -0,0 +1,249 @@
+from pprint import pprint
+
+import os
+import re
+import shutil
+import tempfile
+
+from skimage.metrics import normalized_mutual_information
+
+import itk
+
+NumberOfIterations = 2100
+# NumberOfIterations = 4000
+
+metric_patern = r'Final metric value = (\S+)'
+metric_prog = re.compile(metric_patern)
+
+
+
+class elastix_reg:
+
+
+ def register_aux(self, fi, mv, debug=False, MaximumNumberOfIterations=[str(NumberOfIterations)]):
+
+ parameter_object = itk.ParameterObject.New()
+ default_rigid_parameter_map = parameter_object.GetDefaultParameterMap('rigid')
+ default_rigid_parameter_map["AutomaticTransformInitialization"] = ["true"]
+ # default_rigid_parameter_map["NumberOfSamplesForExactGradient"] = ["100000"]
+ default_rigid_parameter_map['MaximumNumberOfIterations'] = MaximumNumberOfIterations
+ parameter_object.AddParameterMap(default_rigid_parameter_map)
+
+ # pprint(default_rigid_parameter_map.asdict())
+ # exit()
+
+ outdir1 = tempfile.mkdtemp()
+
+ try:
+ fm, params1 = itk.elastix_registration_method(
+ fi, mv,
+ parameter_object=parameter_object,
+ # log_to_console=True,
+ log_to_file=True,
+ output_directory = outdir1,
+ )
+ except Exception as ex:
+ print(ex)
+ print(os.path.join(outdir1, 'elastix.log'))
+ # exit()
+ return {
+ 'metrics': 0,
+ }
+
+ TransformParameterFileName = os.path.join(outdir1, 'TransformParameters.0.txt')
+
+ # print(TransformParameterFileName)
+ # exit()
+
+ '''
+ The DisplacementMagnitudePenalty is a cost function that penalises ||Tμ(x) − x||2. You can use this
+ to invert transforms, by setting the transform to be inverted as an initial transform (using -t0), setting
+ (HowToCombineTransforms "Compose"), and running elastix with this metric, using the original fixed
+ image set both as fixed (-f) and moving (-m) image. After that you can manually set the initial transform
+ in the last parameter file to "NoInitialTransform", and voila, you have the inverse transform! Strictly
+ speaking, you should then also change the Size/Spacing/Origin/Index/Direction settings to match that of
+ the moving image. Select it with:
+ (Metric "DisplacementMagnitudePenalty")
+ Note that inverting a transformation becomes conceptually very similar to performing an image registration
+ in this way. Consequently, the same choices are relevant: optimisation algorithm, multiresolution etc...
+ Note that this procedure was described and evaluated in Metz et al. [2011].
+ '''
+
+ parameter_object2 = itk.ParameterObject.New()
+ inverse_rigid_parameter_map = parameter_object.GetDefaultParameterMap('rigid')
+ inverse_rigid_parameter_map["HowToCombineTransforms"] = ["Compose"]
+ inverse_rigid_parameter_map["Metric"] = ["DisplacementMagnitudePenalty"]
+
+ # inverse_rigid_parameter_map["AutomaticTransformInitialization"] = ["true"]
+ inverse_rigid_parameter_map['MaximumNumberOfIterations'] = MaximumNumberOfIterations
+ # inverse_rigid_parameter_map['UseAdaptiveStepSizes'] = ['false']
+ parameter_object2.AddParameterMap(inverse_rigid_parameter_map)
+
+
+ # print(TransformParameterFileName)
+ # exit()
+
+
+ outdir2 = tempfile.mkdtemp()
+ mm, params2 = itk.elastix_registration_method(
+ mv, mv,
+ parameter_object=parameter_object2,
+ initial_transform_parameter_file_name = TransformParameterFileName,
+ log_to_console=debug,
+ log_to_file=True,
+ output_directory = outdir2,
+ )
+
+ elastix_log = os.path.join(outdir2, 'elastix.log')
+ with open(elastix_log) as log:
+ m = re.search(metric_prog, log.read())
+
+ DisplacementMagnitudePenalty = float(m[1])
+ # print(DisplacementMagnitudePenalty)
+ # exit()
+
+ last_parameter_map = params2.GetParameterMap(0)
+ # pprint(last_parameter_map.asdict())
+ # exit()
+ last_parameter_map["InitialTransformParametersFileName"] = ["NoInitialTransform"]
+
+ params2.SetParameterMap(0, last_parameter_map)
+ # params2.WriteParameterFile('123.txt')
+ mf = itk.transformix_filter(
+ fi,
+ params2)
+
+ m1 = normalized_mutual_information(itk.GetArrayViewFromImage(fi), itk.GetArrayViewFromImage(fm))
+ m2 = normalized_mutual_information(itk.GetArrayViewFromImage(mv), itk.GetArrayViewFromImage(mf))
+
+ print(MaximumNumberOfIterations, m1, m2, DisplacementMagnitudePenalty)
+
+ shutil.rmtree(outdir1)
+ shutil.rmtree(outdir2)
+ # exit()
+
+
+ return {
+ 'fwdtransforms': params1,
+ 'invtransforms': params2,
+ 'warpedfixout': mf,
+ 'warpedmovout': fm,
+ 'metrics': max(m1, m2),
+ 'DisplacementMagnitudePenalty': DisplacementMagnitudePenalty,
+ }
+
+
+ # PixelType = itk.F
+ # Dimension = 3
+ # ImageType = itk.Image[PixelType, Dimension]
+
+
+ # METRIC_THRESHOLD = 1.1
+ def __init__(self, fi, mv, warpedfixout=None, warpedmovout=None, debug=False, iterations_init=NumberOfIterations):
+
+ # reader = itk.ImageFileReader[ImageType].New()
+ # reader.SetFileName(fi)
+ # reader.Update()
+ # fixed_image = reader.GetOutput()
+
+ fixed_image = itk.imread(fi, itk.F)
+ moving_image = itk.imread(mv, itk.F)
+
+ iterations = iterations_init
+ # iterations_fin = iterations_init*2
+
+
+ while True:
+ MaximumNumberOfIterations = [str(iterations)]
+ r1 = self.register_aux(fixed_image, moving_image, debug, MaximumNumberOfIterations=MaximumNumberOfIterations)
+
+ if 'DisplacementMagnitudePenalty' not in r1: # None?
+ break
+ if r1['DisplacementMagnitudePenalty'] < 1:
+ break
+ # elif r1['metrics'] > METRIC_THRESHOLD:
+ # Redo = False
+
+ # if iterations>iterations_fin:
+ # Redo = False
+
+ iterations *= 2
+
+
+ while True:
+ MaximumNumberOfIterations = [str(iterations)]
+ r2 = self.register_aux(moving_image, fixed_image, debug, MaximumNumberOfIterations=MaximumNumberOfIterations)
+
+ if 'DisplacementMagnitudePenalty' not in r2: # None?
+ break
+ elif r2['DisplacementMagnitudePenalty'] < 1:
+ break
+ # elif r2['metrics'] > METRIC_THRESHOLD:
+ # Redo = False
+
+ # if iterations>iterations_fin:
+ # Redo = False
+
+ iterations *= 2
+
+
+
+ if r1['metrics'] > r2['metrics']:
+ self.res = r1
+ else:
+
+ if 'invtransforms' not in r2:
+ return None
+
+ self.res = dict(r2)
+ self.res.update({
+ 'fwdtransforms': r2['invtransforms'],
+ 'invtransforms': r2['fwdtransforms'],
+ 'warpedfixout': r2['warpedmovout'],
+ 'warpedmovout': r2['warpedfixout'],
+ })
+
+
+ assert self.res['DisplacementMagnitudePenalty'] < 1, 'DisplacementMagnitudePenalty: %f ' % (self.res['DisplacementMagnitudePenalty'])
+
+
+ if warpedfixout is not None:
+ itk.imwrite(self.res['warpedfixout'], warpedfixout)
+ if warpedmovout is not None:
+ itk.imwrite(self.res['warpedmovout'], warpedmovout)
+
+ if debug:
+ pprint(self.res)
+ itk.imwrite(fixed_image, '0fixed.nii.gz')
+ itk.imwrite(moving_image, '0moving.nii.gz')
+ itk.imwrite(r1['warpedfixout'], '0mf1.nii.gz')
+ itk.imwrite(r1['warpedmovout'], '0fm1.nii.gz')
+ itk.imwrite(r2['warpedmovout'], '0mf2.nii.gz')
+ itk.imwrite(r2['warpedfixout'], '0fm2.nii.gz')
+
+ # return res
+
+ def get_metrics(self):
+ return self.res['metrics']
+
+ def transform(self, moving, output_filename, is_label=False):
+ transform1 = self.res['fwdtransforms']
+ mv = itk.imread(moving)
+ last_parameter_map = transform1.GetParameterMap(0)
+
+ if is_label:
+ # last_parameter_map["InitialTransformParametersFileName"] = ["NoInitialTransform"]
+ last_parameter_map["ResampleInterpolator"] = ["FinalNearestNeighborInterpolator"]
+ # last_parameter_map["ResultImagePixelType"] = ["unsigned char"]
+
+ t2 = itk.ParameterObject.New()
+ t2.AddParameterMap(last_parameter_map)
+ # pprint(t2.GetParameterMap(0).asdict())
+
+ output = itk.transformix_filter(
+ mv.astype(itk.F),
+ t2)
+
+ if is_label:
+ output=output.astype(itk.UC)
+ itk.imwrite(output, output_filename)
diff --git a/tjfrlfp4.mat b/tjfrlfp4.mat
new file mode 100644
index 0000000..dd0312d
Binary files /dev/null and b/tjfrlfp4.mat differ
+
+ Masonite 4
+
+
+
+
+