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by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + 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GMT","etag":"\"96455b475ba85a33d3d3122d9f0e0f16\"","last-modified":"Sat, 07 May 2022 01:15:09 GMT","vary":"accept-encoding, accept"}}} \ No newline at end of file diff --git a/.python_history b/.python_history new file mode 100644 index 0000000..871bff6 --- /dev/null +++ b/.python_history @@ -0,0 +1,20 @@ +import itk +parameter_object = itk.ParameterObject.New() +import itk +parameter_object = itk.ParameterObject.New() +import itk +itk.version +itk.VERSION +import itk +parameter_object = itk.ParameterObject.New() +from registration.best_reg import registration +from registration import +from registration.best_reg import registration +import monai +monai +dir(monai) +monai._version +monai._version() +monai._version +print(monai._version) +monai.__version__ diff --git a/.wget-hsts b/.wget-hsts new file mode 100644 index 0000000..2b8f815 --- /dev/null +++ b/.wget-hsts @@ -0,0 +1,5 @@ +# HSTS 1.0 Known Hosts database for GNU Wget. +# Edit at your own risk. +# +raw.githubusercontent.com 0 0 1691530822 31536000 +github.com 0 1 1691530822 31536000 diff --git a/1-move.py b/1-move.py index c47dbef..bba798e 100755 --- a/1-move.py +++ b/1-move.py @@ -1,13 +1,19 @@ #!/usr/bin/env python3 import os +import pprint import sys import time from pydicom.dataset import Dataset from pynetdicom import AE, evt, StoragePresentationContexts, debug_logger -from pynetdicom.sop_class import PatientRootQueryRetrieveInformationModelMove +from pynetdicom.sop_class import ( + PatientRootQueryRetrieveInformationModelFind, + PatientRootQueryRetrieveInformationModelMove, + StudyRootQueryRetrieveInformationModelMove, + PatientStudyOnlyQueryRetrieveInformationModelMove, +) # debug_logger() @@ -16,12 +22,13 @@ Series = {} dcm_dir = '/nn' def handle_store(event): - # print(event) +# print(event) """Handle a C-STORE request event.""" ds = event.dataset ds.file_meta = event.file_meta - # print(ds.SeriesInstanceUID) +# print(ds.SeriesInstanceUID) +# print(ds) if ds.SeriesInstanceUID in Series: s = Series[ds.SeriesInstanceUID] @@ -55,13 +62,97 @@ def handle_store(event): # 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)] + handlers = [ + (evt.EVT_C_STORE, handle_store), + ] +# debug_logger() + + StudyInstanceUID_DICT = {} + + 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: + +# d = {} + +# d['StudyDate' ] = FindElement(identifier, '00080020') +# d['ModalitiesInStudy'] = FindElement(identifier, '00080061') +# d['StudyInstanceUID' ] = FindElement(identifier, '0020000D') +# print(d) + +# if (d['ModalitiesInStudy' ] not in StudyInstanceUID_DICT) or ( +# d['StudyDate' ] > StudyInstanceUID_DICT[d['ModalitiesInStudy']]['StudyDate']): +# StudyInstanceUID_DICT[d['ModalitiesInStudy']] = d + + +# print(dir(identifier)) +# print(identifier.keys()) + + + + for sq in identifier[(0x3109, 0x1035)]: +# print(sq) +# print(type(sq)) + # exit() + d = {} + + d['StudyDate' ] = FindElement(sq, '00080020') + d['ModalitiesInStudy'] = FindElement(sq, '00080061') + d['StudyInstanceUID' ] = FindElement(sq, '0020000D') + print(d) + + if (d['ModalitiesInStudy' ] not in StudyInstanceUID_DICT) or ( + d['StudyDate' ] > StudyInstanceUID_DICT[d['ModalitiesInStudy']]['StudyDate']): + StudyInstanceUID_DICT[d['ModalitiesInStudy']] = d + + + assoc.release() + pprint.pprint(StudyInstanceUID_DICT) +# exit() + + + # Initialise the Application Entity ae = AE() - # Add a requested presentation context ae.add_requested_context(PatientRootQueryRetrieveInformationModelMove) @@ -73,34 +164,40 @@ def QueryDCM(PatientID): # 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) - # Create out identifier (query) dataset - ds = Dataset() - ds.QueryRetrieveLevel = 'PATIENT' - ds.PatientID = PatientID + for ModalitiesInStudy, d in StudyInstanceUID_DICT.items(): + StudyInstanceUID = d['StudyInstanceUID'] + + # 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) - # 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', - ) + # 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') - - if assoc.is_established: - # Use the C-MOVE service to send the identifier - responses = assoc.send_c_move(ds, 'OUR_STORE_SCP', PatientRootQueryRetrieveInformationModelMove) - - 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') + # Release the association + assoc.release() + else: + print('Association rejected, aborted or never connected') # Stop our Storage SCP scp.shutdown() diff --git a/2-infer.py b/2-infer.py index 9e42ac3..ba6815a 100755 --- a/2-infer.py +++ b/2-infer.py @@ -1,5 +1,26 @@ #!/usr/bin/env python3 +''' +2d 0.4610997436727624 +3d_fullres 0.5022740762294419 +3d_lowres 0.5957028945994233 +3d_cascade_fullres 0.517286480153028 +ensemble_2d__nnUNetTrainerV2__nnUNetPlansv2.1--3d_fullres__nnUNetTrainerV2__nnUNetPlansv2.1 0.5243185547220239 +ensemble_2d__nnUNetTrainerV2__nnUNetPlansv2.1--3d_lowres__nnUNetTrainerV2__nnUNetPlansv2.1 0.552552255340162 +ensemble_2d__nnUNetTrainerV2__nnUNetPlansv2.1--3d_cascade_fullres__nnUNetTrainerV2CascadeFullRes__nnUNetPlansv2.1 0.531701751318307 +ensemble_3d_fullres__nnUNetTrainerV2__nnUNetPlansv2.1--3d_lowres__nnUNetTrainerV2__nnUNetPlansv2.1 0.6105215496684026 +ensemble_3d_fullres__nnUNetTrainerV2__nnUNetPlansv2.1--3d_cascade_fullres__nnUNetTrainerV2CascadeFullRes__nnUNetPlansv2.1 0.5343679184080806 +ensemble_3d_lowres__nnUNetTrainerV2__nnUNetPlansv2.1--3d_cascade_fullres__nnUNetTrainerV2CascadeFullRes__nnUNetPlansv2.1 0.6000630104223947 +Task222_ICTS2022 submit model ensemble_3d_fullres__nnUNetTrainerV2__nnUNetPlansv2.1--3d_lowres__nnUNetTrainerV2__nnUNetPlansv2.1 0.6105215496684026 + +Here is how you should predict test cases. Run in sequential order and replace all input and output folder names with your personalized ones + +nnUNet_predict -i FOLDER_WITH_TEST_CASES -o OUTPUT_FOLDER_MODEL1 -tr nnUNetTrainerV2 -ctr nnUNetTrainerV2CascadeFullRes -m 3d_fullres -p nnUNetPlansv2.1 -t Task222_ICTS2022 +nnUNet_predict -i FOLDER_WITH_TEST_CASES -o OUTPUT_FOLDER_MODEL2 -tr nnUNetTrainerV2 -ctr nnUNetTrainerV2CascadeFullRes -m 3d_lowres -p nnUNetPlansv2.1 -t Task222_ICTS2022 +nnUNet_ensemble -f OUTPUT_FOLDER_MODEL1 OUTPUT_FOLDER_MODEL2 -o OUTPUT_FOLDER -pp /workspace/nnUNet_trained_models/nnUNet/ensembles/Task222_ICTS2022/ensemble_3d_fullres__nnUNetTrainerV2__nnUNetPlansv2.1--3d_lowres__nnUNetTrainerV2__nnUNetPlansv2.1/postprocessing.json +''' + + import difflib import os import shutil @@ -8,14 +29,16 @@ import sys import time from nipype.interfaces.dcm2nii import Dcm2niix +from pydicom import dcmread +from pynetdicom import AE, debug_logger +from pynetdicom.sop_class import CTImageStorage, RTStructureSetStorage from rt_utils import RTStructBuilder import numpy as np import SimpleITK as sitk - -import itk_elastix - +# import itk_elastix +from registration.best_reg import reg_transform def dcm2nii(source_dir, output_dir): @@ -30,13 +53,17 @@ def dcm2nii(source_dir, output_dir): converter.run() -def register(DCM_CT, DCM_MR): +def inference(DCM_CT, DCM_MR): matcher = difflib.SequenceMatcher(a=DCM_CT, b=DCM_MR) match = matcher.find_longest_match(0, len(matcher.a), 0, len(matcher.b)) ROOT_DIR = DCM_CT[:match.size] NII_DIR = os.path.join(ROOT_DIR, 'nii') INPUT_DIR = os.path.join(ROOT_DIR, 'input') + + OUTPUT_3d_fullres = os.path.join(ROOT_DIR, '3d_fullres') + OUTPUT_3d_lowres = os.path.join(ROOT_DIR, '3d_lowres') + OUTPUT_DIR = os.path.join(ROOT_DIR, 'output') head, tail = os.path.split(DCM_CT) @@ -46,6 +73,8 @@ def register(DCM_CT, DCM_MR): os.makedirs(NII_DIR) shutil.rmtree(INPUT_DIR, ignore_errors=True) os.makedirs(INPUT_DIR) + shutil.rmtree(OUTPUT_3d_fullres, ignore_errors=True) + shutil.rmtree(OUTPUT_3d_lowres, ignore_errors=True) shutil.rmtree(OUTPUT_DIR, ignore_errors=True) # os.makedirs(OUTPUT_DIR) @@ -80,6 +109,7 @@ def register(DCM_CT, DCM_MR): print(NII_CT, NII_MR, input_file) # nnUNet_predict -i INPUT_FOLDER -o OUTPUT_FOLDER -t 222 -m 3d_lowres --save_npz + ''' subprocess.run(["nnUNet_predict", "-i", INPUT_DIR, "-o", OUTPUT_DIR, @@ -87,11 +117,56 @@ def register(DCM_CT, DCM_MR): "-m", "3d_lowres", "--save_npz", ]) + ''' + +# nnUNet_predict -i FOLDER_WITH_TEST_CASES -o OUTPUT_FOLDER_MODEL1 -tr nnUNetTrainerV2 -ctr nnUNetTrainerV2CascadeFullRes -m 3d_fullres -p nnUNetPlansv2.1 -t Task222_ICTS2022 +# nnUNet_predict -i FOLDER_WITH_TEST_CASES -o OUTPUT_FOLDER_MODEL2 -tr nnUNetTrainerV2 -ctr nnUNetTrainerV2CascadeFullRes -m 3d_lowres -p nnUNetPlansv2.1 -t Task222_ICTS2022 +# nnUNet_ensemble -f OUTPUT_FOLDER_MODEL1 OUTPUT_FOLDER_MODEL2 -o OUTPUT_FOLDER -pp /workspace/nnUNet_trained_models/nnUNet/ensembles/Task222_ICTS2022/ensemble_3d_fullres__nnUNetTrainerV2__nnUNetPlansv2.1--3d_lowres__nnUNetTrainerV2__nnUNetPlansv2.1/postprocessing.json + + + subprocess.run(["nnUNet_predict", + "-i", INPUT_DIR, + "-o", OUTPUT_3d_fullres, + "-tr", "nnUNetTrainerV2", + "-ctr", "nnUNetTrainerV2CascadeFullRes", + "-m", "3d_fullres", + "-p", "nnUNetPlansv2.1", + "-t", "Task222_ICTS2022", + "--save_npz", + ]) + + subprocess.run(["nnUNet_predict", + "-i", INPUT_DIR, + "-o", OUTPUT_3d_lowres, + "-tr", "nnUNetTrainerV2", + "-ctr", "nnUNetTrainerV2CascadeFullRes", + "-m", "3d_lowres", + "-p", "nnUNetPlansv2.1", + "-t", "Task222_ICTS2022", + "--save_npz", + ]) + + a = ["nnUNet_ensemble", + "-f", OUTPUT_3d_fullres, OUTPUT_3d_lowres, + "-o", OUTPUT_DIR, + "-pp", "/workspace/nnUNet_trained_models/nnUNet/ensembles/Task222_ICTS2022/ensemble_3d_fullres__nnUNetTrainerV2__nnUNetPlansv2.1--3d_lowres__nnUNetTrainerV2__nnUNetPlansv2.1/postprocessing.json", + ] + + print (' '.join(a)) + + subprocess.run(["nnUNet_ensemble", + "-f", OUTPUT_3d_fullres, OUTPUT_3d_lowres, + "-o", OUTPUT_DIR, + "-pp", "/workspace/nnUNet_trained_models/nnUNet/ensembles/Task222_ICTS2022/ensemble_3d_fullres__nnUNetTrainerV2__nnUNetPlansv2.1--3d_lowres__nnUNetTrainerV2__nnUNetPlansv2.1/postprocessing.json", + ]) + print(output_file) - r2 = itk_elastix.register(NII_CT, NII_MR) - itk_elastix.transform_write(output_file, r2['fwdtransforms'], label_file, is_label=True) +# r2 = itk_elastix.register(NII_CT, NII_MR) +# itk_elastix.transform_write(output_file, r2['fwdtransforms'], label_file, is_label=True) + + reg_transform(NII_CT, NII_MR, output_file, label_file) reader = sitk.ImageSeriesReader() dicom_names = reader.GetGDCMSeriesFileNames(DCM_CT) @@ -126,8 +201,48 @@ def register(DCM_CT, DCM_MR): print(rtss_file) rtstruct.save(rtss_file) + + return rtss_file +# incorporate send_c_store + +def SendDCM(fp): + debug_logger() + + # Initialise the Application Entity + ae = AE() + ae.ae_title = 'OUR_STORE_SCP' + + # Add a requested presentation context + # ae.add_requested_context(CTImageStorage) + ae.add_requested_context(RTStructureSetStorage) + + # Read in our DICOM CT dataset + ds = dcmread(fp) + + # Associate with peer AE at IP 127.0.0.1 and port 11112 + assoc = ae.associate("127.0.0.1", 11112) + assoc = ae.associate("172.16.40.36", 104, + ae_title = 'N1000_STORAGE', + ) + if assoc.is_established: + # Use the C-STORE service to send the dataset + # returns the response status as a pydicom Dataset + status = assoc.send_c_store(ds) + + # Check the status of the storage request + if status: + # If the storage request succeeded this will be 0x0000 + print('C-STORE request 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') + def main(): if len(sys.argv) < 2: @@ -138,7 +253,8 @@ def main(): print(sys.argv[1]) start = time.time() - register(sys.argv[1], sys.argv[2]) + rtss_file = inference(sys.argv[1], sys.argv[2]) + SendDCM(rtss_file) end = time.time() print(end - start, 'seconds') diff --git a/6jj_lths.mat b/6jj_lths.mat new file mode 100644 index 0000000000000000000000000000000000000000..b09b4502f3d09f87e567f51dec22a92fbf948178 GIT binary patch literal 193 zcmZQzU|`?@Vn!ea0cjw1OiRnmOARSX%qvdIFUpNi$uCXHNsTv-HwLMA@c-X?dmw#a zrdjuXAe|s_rvXGOsQm8)i9b+$1D1DSYuyMEXGmSw1QI{6pmrmOR%n69GjPR79{};~ xncN(JbVJStO%Tn%48$Jqu9!M{E z<=6$H54`_hv>(J5+|&i48(hDFJoTkR)T1UhY> /etc/environment && bash #EXPOSE 22 +# Masonite +EXPOSE 8000 + # jupyter ENTRYPOINT jupyter-lab EXPOSE 8888 # pynetdicom EXPOSE 11120 - -# WORKDIR /workspace -WORKDIR /123 diff --git a/docker/qrun.sh b/docker/qrun.sh index d5ab395..856bc9c 100755 --- a/docker/qrun.sh +++ b/docker/qrun.sh @@ -4,11 +4,20 @@ export dockerImage=123:v0 #docker run --gpus all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 -it --rm -v $DIR:/workspace $dockerImage /bin/bash -GPU=nvidia0 gpu-docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 -it --rm \ +# GPU=nvidia0 gpu-docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 -it --rm \ +#GPU=nvidia0 gpu-docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \ +docker run --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 \ +--name 123 \ -v /share/WORKSPACE/nnUNet:/workspace \ -v /share/Public/git/123:/123 \ -v /share/Public/git/123:/root \ -v /share/Public/nn:/nn \ --p 11120:11120 \ +-v /share/Public/Patient:/Patient \ +-p 8000:8000 \ -p 8888:8888 \ +-p 11120:11120 \ $dockerImage & + + +# Then recreate, adding GPU in runtime + diff --git a/docker/requirements.txt b/docker/requirements.txt new file mode 100644 index 0000000..70fbb58 --- /dev/null +++ b/docker/requirements.txt @@ -0,0 +1,2 @@ +masonite>=4.0,<5.0 +masonite-orm>=2.0,<3.0 diff --git a/myapp/.env-example b/myapp/.env-example new file mode 100644 index 0000000..9499e35 --- /dev/null +++ b/myapp/.env-example @@ -0,0 +1,51 @@ +APP_DEBUG=True +APP_ENV=local +APP_KEY=kdFqv3GDtbgryi-1RAtMDwFa80WQuDPwYcFDie4r9zs= +APP_URL=http://localhost:8000 +HASHING_FUNCTION=bcrypt +MIX_BASE_URL= + +MAIL_DRIVER=terminal +MAIL_FROM= +MAIL_HOST= +MAIL_PORT= +MAIL_USERNAME= +MAIL_PASSWORD= + +MAILGUN_DOMAIN= +MAILGUN_SECRET= + +DB_CONNECTION=sqlite +SQLITE_DB_DATABASE=masonite.sqlite3 +DB_HOST=127.0.0.1 +DB_USERNAME=root +DB_PASSWORD=root +DB_DATABASE=masonite +DB_PORT=3306 +DB_LOG=True + +S3_CLIENT= +S3_SECRET= +S3_BUCKET= + +JWT_SECRET= + +QUEUE_DRIVER=async +QUEUE_USERNAME= +QUEUE_VHOST= +QUEUE_PASSWORD= +QUEUE_HOST= +QUEUE_PORT= +QUEUE_CHANNEL= + +SLACK_TOKEN= +SLACK_WEBHOOK= + +VONAGE_KEY= +VONAGE_SECRET= +VONAGE_SMS_FROM= + +PUSHER_CLIENT= +PUSHER_APP_ID= +PUSHER_SECRET= +PUSHER_CLUSTER= \ No newline at end of file diff --git a/myapp/.env.testing b/myapp/.env.testing new file mode 100644 index 0000000..1ad83c1 --- /dev/null +++ b/myapp/.env.testing @@ -0,0 +1,2 @@ +DB_CONNECTION=sqlite +DB_LOG=True \ No newline at end of file diff --git a/myapp/.gitignore b/myapp/.gitignore new file mode 100644 index 0000000..4d928ff --- /dev/null +++ b/myapp/.gitignore @@ -0,0 +1,18 @@ +# python +*.pyc +*__pycache__ +.pytest_cache +venv +# environment +.env +.env.* +!.env.testing +# npm +node_modules +package-lock.json + +.vscode +**/*.DS_Store + +# compiled assets +storage/compiled diff --git a/myapp/Kernel.py b/myapp/Kernel.py new file mode 100644 index 0000000..9bb3f4c --- /dev/null +++ b/myapp/Kernel.py @@ -0,0 +1,117 @@ +from masonite.foundation import response_handler +from masonite.storage import StorageCapsule +from masonite.auth import Sign +from masonite.environment import LoadEnvironment +from masonite.utils.structures import load +from masonite.utils.location import base_path +from masonite.middleware import ( + SessionMiddleware, + EncryptCookies, + LoadUserMiddleware, + MaintenanceModeMiddleware, +) +from masonite.routes import Route +from masonite.configuration.Configuration import Configuration +from masonite.configuration import config + +from app.middlewares import VerifyCsrfToken, AuthenticationMiddleware +from masonite.api.middleware import JWTAuthenticationMiddleware + +class Kernel: + + http_middleware = [MaintenanceModeMiddleware, EncryptCookies] + + route_middleware = { + "web": [SessionMiddleware, LoadUserMiddleware, VerifyCsrfToken], + "auth": [AuthenticationMiddleware], + + # .. + "api": [ + JWTAuthenticationMiddleware + ], + + } + + def __init__(self, app): + self.application = app + + def register(self): + # Register routes + self.load_environment() + self.register_configurations() + self.register_middleware() + self.register_routes() + self.register_database() + self.register_templates() + self.register_storage() + + def load_environment(self): + LoadEnvironment() + + def register_configurations(self): + # load configuration + self.application.bind("config.location", "config") + configuration = Configuration(self.application) + configuration.load() + self.application.bind("config", configuration) + key = config("application.key") + self.application.bind("key", key) + self.application.bind("sign", Sign(key)) + # set locations + self.application.bind("resources.location", "resources/") + self.application.bind("controllers.location", "app/controllers") + self.application.bind("jobs.location", "app/jobs") + self.application.bind("providers.location", "app/providers") + self.application.bind("mailables.location", "app/mailables") + self.application.bind("listeners.location", "app/listeners") + self.application.bind("validation.location", "app/validation") + self.application.bind("notifications.location", "app/notifications") + self.application.bind("events.location", "app/events") + self.application.bind("tasks.location", "app/tasks") + self.application.bind("models.location", "app/models") + self.application.bind("observers.location", "app/models/observers") + self.application.bind("policies.location", "app/policies") + self.application.bind("commands.location", "app/commands") + self.application.bind("middlewares.location", "app/middlewares") + + self.application.bind("server.runner", "masonite.commands.ServeCommand.main") + + def register_middleware(self): + self.application.make("middleware").add(self.route_middleware).add(self.http_middleware) + + def register_routes(self): + Route.set_controller_locations(self.application.make("controllers.location")) + self.application.bind("routes.location", "routes/web") + self.application.make("router").add( + Route.group( + load(self.application.make("routes.location"), "ROUTES"), middleware=["web"] + ) + ) + #API Development + self.application.bind("routes.api.location", "routes/api") + + + + def register_database(self): + from masoniteorm.query import QueryBuilder + + self.application.bind( + "builder", + QueryBuilder(connection_details=config("database.databases")), + ) + + self.application.bind("migrations.location", "databases/migrations") + self.application.bind("seeds.location", "databases/seeds") + + self.application.bind("resolver", config("database.db")) + + def register_templates(self): + self.application.bind("views.location", "templates/") + + def register_storage(self): + storage = StorageCapsule() + storage.add_storage_assets(config("filesystem.staticfiles")) + self.application.bind("storage_capsule", storage) + + self.application.set_response_handler(response_handler) + self.application.use_storage_path(base_path("storage")) diff --git a/myapp/app/__init__.py b/myapp/app/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/myapp/app/controllers/BlogController.py b/myapp/app/controllers/BlogController.py new file mode 100644 index 0000000..8aeb19c --- /dev/null +++ b/myapp/app/controllers/BlogController.py @@ -0,0 +1,7 @@ +from masonite.controllers import Controller +from masonite.views import View + + +class BlogController(Controller): + def show(self, view: View): + return view.render("blog") diff --git a/myapp/app/controllers/PatientController.py b/myapp/app/controllers/PatientController.py new file mode 100644 index 0000000..82f916e --- /dev/null +++ b/myapp/app/controllers/PatientController.py @@ -0,0 +1,11 @@ +from masonite.controllers import Controller +from masonite.views import View + + +class PatientController(Controller): + def show(self, view: View): + return view.render("patient.html") + + def move(self, view: View): + return view.render("patient.html") + \ No newline at end of file diff --git a/myapp/app/controllers/WelcomeController.py b/myapp/app/controllers/WelcomeController.py new file mode 100644 index 0000000..28c74b8 --- /dev/null +++ b/myapp/app/controllers/WelcomeController.py @@ -0,0 +1,10 @@ +"""A WelcomeController Module.""" +from masonite.views import View +from masonite.controllers import Controller + + +class WelcomeController(Controller): + """WelcomeController Controller Class.""" + + def show(self, view: View): + return view.render("welcome") diff --git a/myapp/app/controllers/__init__.py b/myapp/app/controllers/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/myapp/app/controllers/api/UsersController.py b/myapp/app/controllers/api/UsersController.py new file mode 100644 index 0000000..1b2f55f --- /dev/null +++ b/myapp/app/controllers/api/UsersController.py @@ -0,0 +1,19 @@ +from masonite.controllers import Controller +from masonite.views import View + + +class UsersController(Controller): + def index(self, view: View): + return view.render("") + + def show(self, view: View): + return view.render("") + + def store(self, view: View): + return view.render("") + + def update(self, view: View): + return view.render("") + + def destroy(self, view: View): + return view.render("") diff --git a/myapp/app/middlewares/AuthenticationMiddleware.py b/myapp/app/middlewares/AuthenticationMiddleware.py new file mode 100644 index 0000000..f00264c --- /dev/null +++ b/myapp/app/middlewares/AuthenticationMiddleware.py @@ -0,0 +1,13 @@ +from masonite.middleware import Middleware + + +class AuthenticationMiddleware(Middleware): + """Middleware to check if the user is logged in.""" + + def before(self, request, response): + if not request.user(): + return response.redirect(name="login") + return request + + def after(self, request, response): + return request diff --git a/myapp/app/middlewares/VerifyCsrfToken.py b/myapp/app/middlewares/VerifyCsrfToken.py new file mode 100644 index 0000000..d1f7b11 --- /dev/null +++ b/myapp/app/middlewares/VerifyCsrfToken.py @@ -0,0 +1,6 @@ +from masonite.middleware import VerifyCsrfToken as Middleware + + +class VerifyCsrfToken(Middleware): + + exempt = [] diff --git a/myapp/app/middlewares/__init__.py b/myapp/app/middlewares/__init__.py new file mode 100644 index 0000000..c88e722 --- /dev/null +++ b/myapp/app/middlewares/__init__.py @@ -0,0 +1,3 @@ +# flake8: noqa: F401 +from .VerifyCsrfToken import VerifyCsrfToken +from .AuthenticationMiddleware import AuthenticationMiddleware diff --git a/myapp/app/models/User.py b/myapp/app/models/User.py new file mode 100644 index 0000000..5c1056f --- /dev/null +++ b/myapp/app/models/User.py @@ -0,0 +1,12 @@ +"""User Model.""" +from masoniteorm.models import Model +from masoniteorm.scopes import SoftDeletesMixin +from masonite.authentication import Authenticates + + +class User(Model, SoftDeletesMixin, Authenticates): + """User Model.""" + + __fillable__ = ["name", "email", "password"] + __hidden__ = ["password"] + __auth__ = "email" diff --git a/myapp/app/providers/AppProvider.py b/myapp/app/providers/AppProvider.py new file mode 100644 index 0000000..2a81f14 --- /dev/null +++ b/myapp/app/providers/AppProvider.py @@ -0,0 +1,12 @@ +from masonite.providers import Provider + + +class AppProvider(Provider): + def __init__(self, application): + self.application = application + + def register(self): + pass + + def boot(self): + pass diff --git a/myapp/app/providers/__init__.py b/myapp/app/providers/__init__.py new file mode 100644 index 0000000..61ae291 --- /dev/null +++ b/myapp/app/providers/__init__.py @@ -0,0 +1,2 @@ +# flake8: noqa: F401 +from .AppProvider import AppProvider diff --git a/myapp/config/__init__.py b/myapp/config/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/myapp/config/api.py b/myapp/config/api.py new file mode 100644 index 0000000..746ac11 --- /dev/null +++ b/myapp/config/api.py @@ -0,0 +1,15 @@ +"""API Config""" +from masonite.environment import env + +from app.models.User import User + +DRIVERS = { + "jwt": { + "algorithm": "HS512", + "secret": env("JWT_SECRET"), + "model": User, + "expires": None, + "authenticates": False, + "version": None, + } +} diff --git a/myapp/config/application.py b/myapp/config/application.py new file mode 100644 index 0000000..4b12a24 --- /dev/null +++ b/myapp/config/application.py @@ -0,0 +1,16 @@ +from masonite.environment import env + + +KEY = env("APP_KEY", "-RkDOqXojJIlsF_I8wWiUq_KRZ0PtGWTOZ676u5HtLg=") + +DEBUG = env("APP_DEBUG", True) + +HASHING = { + "default": env("HASHING_FUNCTION", "bcrypt"), + "bcrypt": {"rounds": 10}, + "argon2": {"memory": 1024, "threads": 2, "time": 2}, +} + +APP_URL = env("APP_URL", "http://localhost:8000/") + +MIX_BASE_URL = env("MIX_BASE_URL", None) diff --git a/myapp/config/auth.py b/myapp/config/auth.py new file mode 100644 index 0000000..c7dadcc --- /dev/null +++ b/myapp/config/auth.py @@ -0,0 +1,8 @@ +from app.models.User import User + +GUARDS = { + "default": "web", + "web": {"model": User}, + "password_reset_table": "password_resets", + "password_reset_expiration": 1440, # in minutes. 24 hours. None if disabled +} diff --git a/myapp/config/broadcast.py b/myapp/config/broadcast.py new file mode 100644 index 0000000..78bc948 --- /dev/null +++ b/myapp/config/broadcast.py @@ -0,0 +1,14 @@ +from masonite.environment import env + + +BROADCASTS = { + "default": "pusher", + "pusher": { + "driver": "pusher", + "client": env("PUSHER_CLIENT"), + "app_id": env("PUSHER_APP_ID"), + "secret": env("PUSHER_SECRET"), + "cluster": env("PUSHER_CLUSTER"), + "ssl": False, + }, +} diff --git a/myapp/config/cache.py b/myapp/config/cache.py new file mode 100644 index 0000000..8623bdb --- /dev/null +++ b/myapp/config/cache.py @@ -0,0 +1,25 @@ +# from masonite.environment import env + + +STORES = { + "default": "local", + "local": { + "driver": "file", + "location": "storage/framework/cache" + # + }, + "redis": { + "driver": "redis", + "host": "127.0.0.1", + "port": "6379", + "password": "", + "name": "project_name", + }, + "memcache": { + "driver": "memcache", + "host": "127.0.0.1", + "port": "11211", + "password": "", + "name": "project_name", + }, +} diff --git a/myapp/config/database.py b/myapp/config/database.py new file mode 100644 index 0000000..091d99f --- /dev/null +++ b/myapp/config/database.py @@ -0,0 +1,56 @@ +from masonite.environment import LoadEnvironment, env +from masoniteorm.connections import ConnectionResolver + +# Loads in the environment variables when this page is imported. +LoadEnvironment() + +""" +The connections here don't determine the database but determine the "connection". +They can be named whatever you want. +""" +DATABASES = { + "default": env("DB_CONNECTION", "sqlite"), + "sqlite": { + "driver": "sqlite", + "database": env("SQLITE_DB_DATABASE", "masonite.sqlite3"), + "prefix": "", + "log_queries": env("DB_LOG"), + }, + "mysql": { + "driver": "mysql", + "host": env("DB_HOST"), + "user": env("DB_USERNAME"), + "password": env("DB_PASSWORD"), + "database": env("DB_DATABASE"), + "port": env("DB_PORT"), + "prefix": "", + "grammar": "mysql", + "options": { + "charset": "utf8mb4", + }, + "log_queries": env("DB_LOG"), + }, + "postgres": { + "driver": "postgres", + "host": env("DB_HOST"), + "user": env("DB_USERNAME"), + "password": env("DB_PASSWORD"), + "database": env("DB_DATABASE"), + "port": env("DB_PORT"), + "prefix": "", + "grammar": "postgres", + "log_queries": env("DB_LOG"), + }, + "mssql": { + "driver": "mssql", + "host": env("MSSQL_DATABASE_HOST"), + "user": env("MSSQL_DATABASE_USER"), + "password": env("MSSQL_DATABASE_PASSWORD"), + "database": env("MSSQL_DATABASE_DATABASE"), + "port": env("MSSQL_DATABASE_PORT"), + "prefix": "", + "log_queries": env("DB_LOG"), + }, +} + +DB = ConnectionResolver().set_connection_details(DATABASES) diff --git a/myapp/config/exceptions.py b/myapp/config/exceptions.py new file mode 100644 index 0000000..0d1f47a --- /dev/null +++ b/myapp/config/exceptions.py @@ -0,0 +1,24 @@ +OPTIONS = { + "editor": "vscode", + "search_url": "https://www.google.com/search?q=", + "links": { + "doc": "https://docs.masoniteproject.com", + "repo": "https://github.com/MasoniteFramework/masonite", + }, + "stack": {"offset": 10, "shorten": True}, + "hide_sensitive_data": True, +} + +HANDLERS = { + "context": True, + "dumps": True, + "solutions": { + "stackoverflow": False, + "possible_solutions": True + }, + "recommendations": { + "packages_updates": { + "list": ["exceptionite", "masonite", "masonite-orm", "pytest"] + } + }, +} diff --git a/myapp/config/filesystem.py b/myapp/config/filesystem.py new file mode 100644 index 0000000..0ede055 --- /dev/null +++ b/myapp/config/filesystem.py @@ -0,0 +1,21 @@ +from masonite.environment import env +from masonite.utils.location import base_path + + +DISKS = { + "default": "local", + "local": {"driver": "file", "path": base_path("storage/framework/filesystem")}, + "s3": { + "driver": "s3", + "client": env("S3_CLIENT"), + "secret": env("S3_SECRET"), + "bucket": env("S3_BUCKET"), + }, +} + +STATICFILES = { + # folder # template alias + "storage/static": "static/", + "storage/compiled": "assets/", + "storage/public": "/", +} diff --git a/myapp/config/mail.py b/myapp/config/mail.py new file mode 100644 index 0000000..2e20dd9 --- /dev/null +++ b/myapp/config/mail.py @@ -0,0 +1,23 @@ +from masonite.environment import env + + +FROM_EMAIL = env("MAIL_FROM", "no-reply@masonite.com") + +DRIVERS = { + "default": env("MAIL_DRIVER", "terminal"), + "smtp": { + "host": env("MAIL_HOST"), + "port": env("MAIL_PORT"), + "username": env("MAIL_USERNAME"), + "password": env("MAIL_PASSWORD"), + "from": FROM_EMAIL, + }, + "mailgun": { + "domain": env("MAILGUN_DOMAIN"), + "secret": env("MAILGUN_SECRET"), + "from": FROM_EMAIL, + }, + "terminal": { + "from": FROM_EMAIL, + }, +} diff --git a/myapp/config/notification.py b/myapp/config/notification.py new file mode 100644 index 0000000..e12dc32 --- /dev/null +++ b/myapp/config/notification.py @@ -0,0 +1,20 @@ +from masonite.environment import env + + +DRIVERS = { + "slack": { + "token": env("SLACK_TOKEN", ""), # used for API mode + "webhook": env("SLACK_WEBHOOK", ""), # used for webhook mode + }, + "vonage": { + "key": env("VONAGE_KEY", ""), + "secret": env("VONAGE_SECRET", ""), + "sms_from": env("VONAGE_SMS_FROM", "+33000000000"), + }, + "database": { + "connection": "sqlite", + "table": "notifications", + }, +} + +DRY = False diff --git a/myapp/config/providers.py b/myapp/config/providers.py new file mode 100644 index 0000000..07e7535 --- /dev/null +++ b/myapp/config/providers.py @@ -0,0 +1,56 @@ +from masonite.providers import ( + RouteProvider, + FrameworkProvider, + ViewProvider, + WhitenoiseProvider, + ExceptionProvider, + MailProvider, + SessionProvider, + QueueProvider, + CacheProvider, + EventProvider, + StorageProvider, + HelpersProvider, + BroadcastProvider, + AuthenticationProvider, + AuthorizationProvider, + HashServiceProvider, + ORMProvider, +) + +# Third Party Providers +from masonite.api.providers import ApiProvider + +from masonite.scheduling.providers import ScheduleProvider +from masonite.notification.providers import NotificationProvider +from masonite.validation.providers import ValidationProvider + +from app.providers import AppProvider + +PROVIDERS = [ + FrameworkProvider, + HelpersProvider, + RouteProvider, + ViewProvider, + WhitenoiseProvider, + ExceptionProvider, + MailProvider, + NotificationProvider, + SessionProvider, + CacheProvider, + QueueProvider, + ScheduleProvider, + EventProvider, + StorageProvider, + BroadcastProvider, + HashServiceProvider, + AuthenticationProvider, + ValidationProvider, + AuthorizationProvider, + ORMProvider, + AppProvider, + + # Third Party Providers + ApiProvider, + +] diff --git a/myapp/config/queue.py b/myapp/config/queue.py new file mode 100644 index 0000000..15f707b --- /dev/null +++ b/myapp/config/queue.py @@ -0,0 +1,39 @@ +from masonite.environment import env + + +DRIVERS = { + "default": env("QUEUE_DRIVER", "async"), + "database": { + "connection": "sqlite", + "table": "jobs", + "failed_table": "failed_jobs", + "attempts": 3, + "poll": 5, + }, + "redis": { + "name": env("QUEUE_USERNAME", "guest"), + "password": env("QUEUE_PASSWORD", "guest"), + "port": env("QUEUE_PORT", "6379"), + "host": env("QUEUE_HOST", "localhost"), + }, + "amqp": { + "username": env("QUEUE_USERNAME", "guest"), + "password": env("QUEUE_PASSWORD", "guest"), + "port": env("QUEUE_PORT", "5672"), + "vhost": env("QUEUE_VHOST", ""), + "host": env("QUEUE_HOST", "localhost"), + "exchange": "", + # See https://pika.readthedocs.io/en/stable/modules/parameters.html#pika.connection.URLParameters + # for valid connection options values + "connection_options": {}, + "channel": env("QUEUE_CHANNEL", "default"), + "queue": "masonite4", + "tz": "UTC", + }, + "async": { + "blocking": True, + "callback": "handle", + "mode": "threading", + "workers": 1, + }, +} diff --git a/myapp/config/session.py b/myapp/config/session.py new file mode 100644 index 0000000..e7557bd --- /dev/null +++ b/myapp/config/session.py @@ -0,0 +1,7 @@ +# from masonite.environment import env + + +DRIVERS = { + "default": "cookie", + "cookie": {}, +} diff --git a/myapp/craft b/myapp/craft new file mode 100644 index 0000000..b32fb5b --- /dev/null +++ b/myapp/craft @@ -0,0 +1,11 @@ +#!/usr/bin/env python +"""Craft Command. +This module is really used for backup only if the masonite CLI cannot import this for you. +This can be used by running "python craft". This module is not ran when the CLI can +successfully import commands for you. +""" + +from wsgi import application + +if __name__ == "__main__": + application.make("commands").run() diff --git a/myapp/databases/migrations/2021_01_09_033202_create_password_reset_table.py b/myapp/databases/migrations/2021_01_09_033202_create_password_reset_table.py new file mode 100644 index 0000000..4fa611f --- /dev/null +++ b/myapp/databases/migrations/2021_01_09_033202_create_password_reset_table.py @@ -0,0 +1,15 @@ +from masoniteorm.migrations import Migration + + +class CreatePasswordResetTable(Migration): + def up(self): + """Run the migrations.""" + with self.schema.create("password_resets") as table: + table.string("email").unique() + table.string("token") + table.datetime("expires_at").nullable() + table.datetime("created_at") + + def down(self): + """Revert the migrations.""" + self.schema.drop("password_resets") diff --git a/myapp/databases/migrations/2021_01_09_043202_create_users_table.py b/myapp/databases/migrations/2021_01_09_043202_create_users_table.py new file mode 100644 index 0000000..3311e59 --- /dev/null +++ b/myapp/databases/migrations/2021_01_09_043202_create_users_table.py @@ -0,0 +1,21 @@ +from masoniteorm.migrations import Migration + + +class CreateUsersTable(Migration): + def up(self): + """Run the migrations.""" + with self.schema.create("users") as table: + table.increments("id") + table.string("name") + table.string("email").unique() + table.string("password") + table.string("second_password").nullable() + table.string("remember_token").nullable() + table.string("phone").nullable() + table.timestamp("verified_at").nullable() + table.timestamps() + table.soft_deletes() + + def down(self): + """Revert the migrations.""" + self.schema.drop("users") diff --git a/myapp/databases/seeds/__init__.py b/myapp/databases/seeds/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/myapp/databases/seeds/database_seeder.py b/myapp/databases/seeds/database_seeder.py new file mode 100644 index 0000000..4baa61b --- /dev/null +++ b/myapp/databases/seeds/database_seeder.py @@ -0,0 +1,10 @@ +"""Base Database Seeder Module.""" +from masoniteorm.seeds import Seeder + +from .user_table_seeder import UserTableSeeder + + +class DatabaseSeeder(Seeder): + def run(self): + """Run the database seeds.""" + self.call(UserTableSeeder) diff --git a/myapp/databases/seeds/user_table_seeder.py b/myapp/databases/seeds/user_table_seeder.py new file mode 100644 index 0000000..bdda61d --- /dev/null +++ b/myapp/databases/seeds/user_table_seeder.py @@ -0,0 +1,18 @@ +"""UserTableSeeder Seeder.""" +from masoniteorm.seeds import Seeder +from masonite.facades import Hash + +from app.models.User import User + + +class UserTableSeeder(Seeder): + def run(self): + """Run the database seeds.""" + User.create( + { + "name": "Joe", + "email": "user@example.com", + "password": Hash.make("secret"), + "phone": "+123456789", + } + ) diff --git a/myapp/makefile b/myapp/makefile new file mode 100644 index 0000000..66a6840 --- /dev/null +++ b/myapp/makefile @@ -0,0 +1,9 @@ +init: + pip install -r requirements.txt +lint: + python -m flake8 . +format: + black . + make lint +serve: + python craft serve diff --git a/myapp/package.json b/myapp/package.json new file mode 100644 index 0000000..800b050 --- /dev/null +++ b/myapp/package.json @@ -0,0 +1,17 @@ +{ + "private": true, + "scripts": { + "dev": "npm run development", + "development": "mix", + "watch": "mix watch", + "watch-poll": "mix watch -- --watch-options-poll=1000", + "hot": "mix watch --hot", + "prod": "npm run production", + "production": "mix --production" + }, + "devDependencies": { + "axios": "^0.22.0", + "laravel-mix": "^6.0.39", + "postcss": "^8.4.5" + } +} diff --git a/myapp/pyproject.toml b/myapp/pyproject.toml new file mode 100644 index 0000000..ddbc992 --- /dev/null +++ b/myapp/pyproject.toml @@ -0,0 +1,11 @@ +[tool.black] +line-length = 99 +target-version = ['py37'] +include = '\.pyi?$' +exclude = '(\.git|\.venv|\.idea|templates|resources|storage|databases\/migrations|node_modules)' + +[tool.pytest.ini_options] +minversion = "6.0" +testpaths = [ + "tests", +] \ No newline at end of file diff --git a/myapp/requirements.txt b/myapp/requirements.txt new file mode 100644 index 0000000..70fbb58 --- /dev/null +++ b/myapp/requirements.txt @@ -0,0 +1,2 @@ +masonite>=4.0,<5.0 +masonite-orm>=2.0,<3.0 diff --git a/myapp/resources/css/app.css b/myapp/resources/css/app.css new file mode 100644 index 0000000..b824a33 --- /dev/null +++ b/myapp/resources/css/app.css @@ -0,0 +1 @@ +/* Put your CSS here */ diff --git a/myapp/resources/js/app.js b/myapp/resources/js/app.js new file mode 100644 index 0000000..683e609 --- /dev/null +++ b/myapp/resources/js/app.js @@ -0,0 +1,2 @@ + +require("./bootstrap.js") diff --git a/myapp/resources/js/bootstrap.js b/myapp/resources/js/bootstrap.js new file mode 100644 index 0000000..9f66ef4 --- /dev/null +++ b/myapp/resources/js/bootstrap.js @@ -0,0 +1,23 @@ +/** + * We'll load the axios HTTP library which allows us to easily issue requests + * to our Masonite back-end. This library automatically handles sending the + * CSRF token as a header based on the value of the "XSRF" token cookie. + */ + +window.axios = require('axios'); + +window.axios.defaults.headers.common['X-Requested-With'] = 'XMLHttpRequest'; + +/** + * Next we will register the CSRF Token as a common header with Axios so that + * all outgoing HTTP requests automatically have it attached. This is just + * a simple convenience so we don't have to attach every token manually. + */ + +let token = document.head.querySelector('meta[name="csrf-token"]'); + +if (token) { + window.axios.defaults.headers.common['X-CSRF-TOKEN'] = token.content; +} else { + console.error('CSRF token not found: https://docs.masoniteproject.com/features/csrf#ajax-vue-axios'); +} diff --git a/myapp/routes/api.py b/myapp/routes/api.py new file mode 100644 index 0000000..dec4e94 --- /dev/null +++ b/myapp/routes/api.py @@ -0,0 +1,7 @@ +# routes/api.py + +from masonite.routes import Route + +ROUTES = [ + Route.get('/users', 'UsersController@index') +] diff --git a/myapp/routes/web.py b/myapp/routes/web.py new file mode 100644 index 0000000..db0f1da --- /dev/null +++ b/myapp/routes/web.py @@ -0,0 +1,14 @@ +from masonite.routes import Route +from masonite.api import Api + +ROUTES = [ +# Route.get("/", "WelcomeController@show"), + Route.get("/", "PatientController@show"), + Route.post("/patient/move", "PatientController@move"), + + # Blog Routes + Route.get('/blog', 'BlogController@show'), + +] + +ROUTES += Api.routes(auth_route="/api/auth", reauth_route="/api/reauth") \ No newline at end of file diff --git a/myapp/setup.cfg b/myapp/setup.cfg new file mode 100644 index 0000000..59c885f --- /dev/null +++ b/myapp/setup.cfg @@ -0,0 +1,8 @@ +[flake8] +max-line-length = 99 +exclude = .git,.venv,.idea,templates,resources,storage,databases/migrations,resources,node_modules,__pycache__ +ignore=E501,F401,E203,E128,E402,E731,F821,E712,W503,F811 + +[coverage:run] +include = backend/* +omit = *migrations*, *tests*, config/*, manage.py, conftest.py diff --git a/myapp/storage/.gitignore b/myapp/storage/.gitignore new file mode 100644 index 0000000..e69de29 diff --git a/myapp/storage/public/favicon.ico b/myapp/storage/public/favicon.ico new file mode 100644 index 0000000000000000000000000000000000000000..fe97996ec72abee50a3b57cf0be7c0b271537d0b GIT binary patch literal 15406 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title %}Masonite 4{% endblock %} + + + {% block head %} + + {% endblock %} + + + {% block content %}{% endblock %} + {% block js %} + + {% endblock %} + + diff --git a/myapp/templates/base.html b/myapp/templates/base.html new file mode 100644 index 0000000..c7998b1 --- /dev/null +++ b/myapp/templates/base.html @@ -0,0 +1,26 @@ + + + + + + + + {% block title %}Masonite 4{% endblock %} + + + + + + {% block head %} + + {% endblock %} + + + {% block content %}{% endblock %} + + + {% block js %} + + {% endblock %} + + diff --git a/myapp/templates/blog.html b/myapp/templates/blog.html new file mode 100644 index 0000000..5690c51 --- /dev/null +++ b/myapp/templates/blog.html @@ -0,0 +1 @@ +This is a blog \ No newline at end of file diff --git a/myapp/templates/errors/403.html b/myapp/templates/errors/403.html new file mode 100644 index 0000000..0435b9f --- /dev/null +++ b/myapp/templates/errors/403.html @@ -0,0 +1,20 @@ + + + + + + + + Permission Denied + + + + + {% block content %} +
+

Oops looks like you don't have access to this page !

+
+ {% 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 @@ + + + + + + + + Page Not Found + + + + + {% block content %} +
+

Oops this page does not exist !

+
+ {% 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 @@ + + + + + + + + Error 500 + + + + + {% block content %} +
+

Oops an error happened !

+
+ {% 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 @@ + + + + + + + + Server Maintenance + + + + + {% block content %} +
+

Sorry, this site is currently down for maintenance.

+
+ {% 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 + +
+ {{ csrf_field }} +
+ + +
Medical record number
+
+ +
+ +@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 %} +
+ Masonite Logo +
+ Masonite 4 +
+ + + +
+{% 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 0000000000000000000000000000000000000000..ebe919eaa109799b54450d8949bfa5f806a009c2 GIT binary patch literal 193 zcmZQzU|`?@Vn!ea0cjw1OiRnmOARSX%qvdIFUpNi$uCXHNsTv-HwG&a+VS2V$Z+tv zdH_T-WN7y62T})`?;HTp4prO1@(hvRCxG}3#>MR*bqDy?OajxA|G@GOJU%cV0E#O# xNIE%y=o~r613;RA8Hi!dVFR+$GAmM3KoSXS7jqr}(hWINR2+b`1IJ(c0|2%AF7yBZ literal 0 HcmV?d00001 diff --git a/razmtoz2.mat b/razmtoz2.mat new file mode 100644 index 0000000000000000000000000000000000000000..992d9c66eee916f2377bb61dbfb4095f1eb01e90 GIT binary patch literal 193 zcmZQzU|`?@Vn!ea0cjw1OiRnmOARSX%qvdIFUpNi$uCXHNsTv-HwLLtkof=J9!NXz z#&_)p38)m+f#?TMgF8Xu3xwZ+ 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 0000000000000000000000000000000000000000..dd0312daef280f6c9ac09eb9638162a706e3b66b GIT binary patch literal 193 zcmZQzU|`?@Vn!ea0cjw1OiRnmOARSX%qvdIFUpNi$uCXHNsTv-HwLL_SoG(;J&;cL zVLb^%A4p}Kz8^%lnN9-JoBo0286Fsfg5(#}vrPxl3