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xfr 2023-08-08 22:04:06 +00:00
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ps aux
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ls /nn
ls -ltr /nn

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# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# C extensions
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# Distribution / packaging
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build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
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MANIFEST
# PyInstaller
# Usually these files are written 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
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htmlcov/
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.nox/
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nosetests.xml
coverage.xml
*.cover
*.py,cover
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*.pot
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*.log
local_settings.py
db.sqlite3
db.sqlite3-journal
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instance/
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# Scrapy stuff:
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target/
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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
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celerybeat-schedule
celerybeat.pid
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.venv
env/
venv/
ENV/
env.bak/
venv.bak/
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# Rope project settings
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/site
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dmypy.json
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# and can be added to the global gitignore or merged into this file. For a more nuclear
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/
*.nii
*.nii.gz

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{
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{
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}

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2022-05-11T03:11:38.961576

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[Trash Info]
Path=/123/myapp/routes/Untitled%20Folder
DeletionDate=2022-06-01T04:13:59

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[Trash Info]
Path=/123/myapp/app/resources
DeletionDate=2022-06-01T04:12:37

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[Trash Info]
Path=/123/myapp/app/resources
DeletionDate=2022-06-01T04:12:05

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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="refresh" content="1;url=http://0.0.0.0:8888/lab" />
<title>Opening Jupyter Notebook</title>
<script>
setTimeout(function() {
window.location.href = "http://0.0.0.0:8888/lab";
}, 1000);
</script>
</head>
<body>
<p>
This page should redirect you to Jupyter Notebook. If it doesn't,
<a href="http://0.0.0.0:8888/lab">click here to go to Jupyter</a>.
</p>
</body>
</html>

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{
"base_url": "/",
"hostname": "0.0.0.0",
"notebook_dir": "/123",
"password": true,
"pid": 1,
"port": 8888,
"secure": false,
"sock": "",
"token": "",
"url": "http://0.0.0.0:8888/"
}

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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__

5
.wget-hsts Normal file
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@ -0,0 +1,5 @@
# HSTS 1.0 Known Hosts database for GNU Wget.
# Edit at your own risk.
# <hostname> <port> <incl. subdomains> <created> <max-age>
raw.githubusercontent.com 0 0 1691530822 31536000
github.com 0 1 1691530822 31536000

151
1-move.py
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@ -1,13 +1,19 @@
#!/usr/bin/env python3 #!/usr/bin/env python3
import os import os
import pprint
import sys import sys
import time import time
from pydicom.dataset import Dataset from pydicom.dataset import Dataset
from pynetdicom import AE, evt, StoragePresentationContexts, debug_logger 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() # debug_logger()
@ -16,12 +22,13 @@ Series = {}
dcm_dir = '/nn' dcm_dir = '/nn'
def handle_store(event): def handle_store(event):
# print(event) # print(event)
"""Handle a C-STORE request event.""" """Handle a C-STORE request event."""
ds = event.dataset ds = event.dataset
ds.file_meta = event.file_meta ds.file_meta = event.file_meta
# print(ds.SeriesInstanceUID) # print(ds.SeriesInstanceUID)
# print(ds)
if ds.SeriesInstanceUID in Series: if ds.SeriesInstanceUID in Series:
s = Series[ds.SeriesInstanceUID] s = Series[ds.SeriesInstanceUID]
@ -55,13 +62,97 @@ def handle_store(event):
# Return a 'Success' status # Return a 'Success' status
return 0x0000 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): 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 # Initialise the Application Entity
ae = AE() ae = AE()
# Add a requested presentation context # Add a requested presentation context
ae.add_requested_context(PatientRootQueryRetrieveInformationModelMove) 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(("127.0.0.1", 11120), block=False, evt_handlers=handlers)
scp = ae.start_server(("0.0.0.0", 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 for ModalitiesInStudy, d in StudyInstanceUID_DICT.items():
ds = Dataset() StudyInstanceUID = d['StudyInstanceUID']
ds.QueryRetrieveLevel = 'PATIENT'
ds.PatientID = PatientID # 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 # Associate with peer AE at IP 127.0.0.1 and port 11112
# assoc = ae.associate("127.0.0.1", 11112) # assoc = ae.associate("127.0.0.1", 11112)
assoc = ae.associate("192.168.10.56", 104, assoc = ae.associate("192.168.10.56", 104,
ae_title = 'IQWEBX', ae_title = 'IQWEBX',
) )
if assoc.is_established:
if assoc.is_established: # Use the C-MOVE service to send the identifier
# Use the C-MOVE service to send the identifier responses = assoc.send_c_move(ds, 'OUR_STORE_SCP', PatientRootQueryRetrieveInformationModelMove)
responses = assoc.send_c_move(ds, 'OUR_STORE_SCP', PatientRootQueryRetrieveInformationModelMove)
for (status, identifier) in responses: # print(responses)
# print(status, identifier) for (status, identifier) in responses:
if status: # print(status, identifier)
print('C-MOVE query status: 0x{0:04x}'.format(status.Status)) if status:
else: print('C-MOVE query status: 0x{0:04x}'.format(status.Status))
print('Connection timed out, was aborted or received invalid response') else:
print('Connection timed out, was aborted or received invalid response')
# Release the association # Release the association
assoc.release() assoc.release()
else: else:
print('Association rejected, aborted or never connected') print('Association rejected, aborted or never connected')
# Stop our Storage SCP # Stop our Storage SCP
scp.shutdown() scp.shutdown()

130
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@ -1,5 +1,26 @@
#!/usr/bin/env python3 #!/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 difflib
import os import os
import shutil import shutil
@ -8,14 +29,16 @@ import sys
import time import time
from nipype.interfaces.dcm2nii import Dcm2niix 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 from rt_utils import RTStructBuilder
import numpy as np import numpy as np
import SimpleITK as sitk import SimpleITK as sitk
# import itk_elastix
import itk_elastix from registration.best_reg import reg_transform
def dcm2nii(source_dir, output_dir): def dcm2nii(source_dir, output_dir):
@ -30,13 +53,17 @@ def dcm2nii(source_dir, output_dir):
converter.run() converter.run()
def register(DCM_CT, DCM_MR): def inference(DCM_CT, DCM_MR):
matcher = difflib.SequenceMatcher(a=DCM_CT, b=DCM_MR) matcher = difflib.SequenceMatcher(a=DCM_CT, b=DCM_MR)
match = matcher.find_longest_match(0, len(matcher.a), 0, len(matcher.b)) match = matcher.find_longest_match(0, len(matcher.a), 0, len(matcher.b))
ROOT_DIR = DCM_CT[:match.size] ROOT_DIR = DCM_CT[:match.size]
NII_DIR = os.path.join(ROOT_DIR, 'nii') NII_DIR = os.path.join(ROOT_DIR, 'nii')
INPUT_DIR = os.path.join(ROOT_DIR, 'input') 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') OUTPUT_DIR = os.path.join(ROOT_DIR, 'output')
head, tail = os.path.split(DCM_CT) head, tail = os.path.split(DCM_CT)
@ -46,6 +73,8 @@ def register(DCM_CT, DCM_MR):
os.makedirs(NII_DIR) os.makedirs(NII_DIR)
shutil.rmtree(INPUT_DIR, ignore_errors=True) shutil.rmtree(INPUT_DIR, ignore_errors=True)
os.makedirs(INPUT_DIR) 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) shutil.rmtree(OUTPUT_DIR, ignore_errors=True)
# os.makedirs(OUTPUT_DIR) # os.makedirs(OUTPUT_DIR)
@ -80,6 +109,7 @@ def register(DCM_CT, DCM_MR):
print(NII_CT, NII_MR, input_file) print(NII_CT, NII_MR, input_file)
# nnUNet_predict -i INPUT_FOLDER -o OUTPUT_FOLDER -t 222 -m 3d_lowres --save_npz # nnUNet_predict -i INPUT_FOLDER -o OUTPUT_FOLDER -t 222 -m 3d_lowres --save_npz
'''
subprocess.run(["nnUNet_predict", subprocess.run(["nnUNet_predict",
"-i", INPUT_DIR, "-i", INPUT_DIR,
"-o", OUTPUT_DIR, "-o", OUTPUT_DIR,
@ -87,11 +117,56 @@ def register(DCM_CT, DCM_MR):
"-m", "3d_lowres", "-m", "3d_lowres",
"--save_npz", "--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) print(output_file)
r2 = itk_elastix.register(NII_CT, NII_MR) # r2 = itk_elastix.register(NII_CT, NII_MR)
itk_elastix.transform_write(output_file, r2['fwdtransforms'], label_file, is_label=True) # 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() reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(DCM_CT) dicom_names = reader.GetGDCMSeriesFileNames(DCM_CT)
@ -127,6 +202,46 @@ def register(DCM_CT, DCM_MR):
print(rtss_file) print(rtss_file)
rtstruct.save(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(): def main():
@ -138,7 +253,8 @@ def main():
print(sys.argv[1]) print(sys.argv[1])
start = time.time() 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() end = time.time()
print(end - start, 'seconds') print(end - start, 'seconds')

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52
adding.py Normal file
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@ -0,0 +1,52 @@
from rt_utils import RTStructBuilder
import matplotlib.pyplot as plt
# Load existing RT Struct. Requires the series path and existing RT Struct path
dicom_series_path = "/nn/6768700/20230106/CT/9/"
rt_struct_list = [
"/nn/6768700/20230106/CT/9-rtss.dcm",
"/nn/6768700/20230106/CT/DCM_1.2.840.114358.189250942524258.20230106112102.643186932766_230109075302/rtss~3~a2381ecc-4b94-40cc-a7aa-41968c54e206.dcm",
]
rtstruct = RTStructBuilder.create_new(dicom_series_path=dicom_series_path)
for rt_struct_path in rt_struct_list:
r = RTStructBuilder.create_from(
dicom_series_path=dicom_series_path,
rt_struct_path=rt_struct_path,
)
for name in r.get_roi_names():
mask_3d = r.get_roi_mask_by_name(name)
rtstruct.add_roi(
mask=mask_3d,
name=name,
)
print(name)
rtstruct.save('/nn/6768700/20230106/CT/new-rt-struct.dcm')
exit()
#Large
rtstruct1 = RTStructBuilder.create_from(
dicom_series_path="/nn/6768700/20230106/CT/9/",
rt_struct_path="/nn/6768700/20230106/CT/9-rtss.dcm"
)
#Small
rtstruct2 = RTStructBuilder.create_from(
dicom_series_path="/nn/6768700/20230106/CT/9/",
rt_struct_path="/nn/6768700/20230106/CT/DCM_1.2.840.114358.189250942524258.20230106112102.643186932766_230109075302/rtss~3~a2381ecc-4b94-40cc-a7aa-41968c54e206.dcm"
)
# print(dir(rtstruct2))
for name in rtstruct2.get_roi_names():
mask_3d = rtstruct2.get_roi_mask_by_name(name)
rtstruct1.add_roi(
mask=mask_3d,
name=name,
)
print(name)

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33
dev/register_rtss.py Executable file
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@ -0,0 +1,33 @@
#!/usr/bin/env python3
import os
from pydicom import dcmread
RTSS = '/Patient/RTSS/66351478_struct_set_2022-10-03_10-00-35.dcm'
ReferenceRoot = '/nn/6635147/20220930/MR'
ds = dcmread(RTSS)
print(ds)
exit()
# print(ds['Frame of Reference UID'])
# print(dir(ds))
FrameOfReferenceUID = ds.FrameOfReferenceUID
print(FrameOfReferenceUID)
for root, dirs, files in os.walk(ReferenceRoot):
for name in files:
dcm = os.path.join(root, name)
print(dcm)
ds = dcmread(dcm)
break
print(ds.SeriesInstanceUID)
# break

16
docker/Dockerfile
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@ -6,10 +6,16 @@ RUN apt-get update -y \
# pip # pip
# RUN pip install antspyx itk-elastix nipype nnunet rt_utils # RUN pip install antspyx itk-elastix nipype nnunet rt_utils
RUN pip install antspyx itk-elastix nnunet # too large .... install first RUN pip install antspyx nipype nnunet # too large .... install first
RUN pip install itk-elastix==0.13.0
RUN pip install --upgrade git+https://github.com/FabianIsensee/hiddenlayer.git@more_plotted_details#egg=hiddenlayer RUN pip install --upgrade git+https://github.com/FabianIsensee/hiddenlayer.git@more_plotted_details#egg=hiddenlayer
RUN pip install git+https://github.com/qurit/rt-utils.git@5bab9ffcc8fe19dd775e940afdc3d8f48f869150 # fix FrameOfReferenceUID RUN pip install git+https://github.com/qurit/rt-utils.git@5bab9ffcc8fe19dd775e940afdc3d8f48f869150 # fix FrameOfReferenceUID
RUN pip install masonite nipype
# WORKDIR /workspace
WORKDIR /123
COPY requirements.txt /123
RUN pip install -r requirements.txt
# nnUNet # nnUNet
@ -24,12 +30,12 @@ ENV RESULTS_FOLDER="/workspace/nnUNet_trained_models"
#ENTRYPOINT service ssh restart && env >> /etc/environment && bash #ENTRYPOINT service ssh restart && env >> /etc/environment && bash
#EXPOSE 22 #EXPOSE 22
# Masonite
EXPOSE 8000
# jupyter # jupyter
ENTRYPOINT jupyter-lab ENTRYPOINT jupyter-lab
EXPOSE 8888 EXPOSE 8888
# pynetdicom # pynetdicom
EXPOSE 11120 EXPOSE 11120
# WORKDIR /workspace
WORKDIR /123

13
docker/qrun.sh
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@ -4,11 +4,20 @@
export dockerImage=123:v0 export dockerImage=123:v0
#docker run --gpus all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 -it --rm -v $DIR:/workspace $dockerImage /bin/bash #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/WORKSPACE/nnUNet:/workspace \
-v /share/Public/git/123:/123 \ -v /share/Public/git/123:/123 \
-v /share/Public/git/123:/root \ -v /share/Public/git/123:/root \
-v /share/Public/nn:/nn \ -v /share/Public/nn:/nn \
-p 11120:11120 \ -v /share/Public/Patient:/Patient \
-p 8000:8000 \
-p 8888:8888 \ -p 8888:8888 \
-p 11120:11120 \
$dockerImage & $dockerImage &
# Then recreate, adding GPU in runtime

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docker/requirements.txt Normal file
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@ -0,0 +1,2 @@
masonite>=4.0,<5.0
masonite-orm>=2.0,<3.0

51
myapp/.env-example Normal file
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@ -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=

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myapp/.env.testing Normal file
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@ -0,0 +1,2 @@
DB_CONNECTION=sqlite
DB_LOG=True

18
myapp/.gitignore vendored Normal file
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@ -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

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myapp/Kernel.py Normal file
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@ -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"))

0
myapp/app/__init__.py Normal file
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7
myapp/app/controllers/BlogController.py Normal file
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@ -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")

11
myapp/app/controllers/PatientController.py Normal file
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@ -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")

10
myapp/app/controllers/WelcomeController.py Normal file
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@ -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")

0
myapp/app/controllers/__init__.py Normal file
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19
myapp/app/controllers/api/UsersController.py Normal file
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@ -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("")

13
myapp/app/middlewares/AuthenticationMiddleware.py Normal file
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@ -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

6
myapp/app/middlewares/VerifyCsrfToken.py Normal file
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@ -0,0 +1,6 @@
from masonite.middleware import VerifyCsrfToken as Middleware
class VerifyCsrfToken(Middleware):
exempt = []

3
myapp/app/middlewares/__init__.py Normal file
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@ -0,0 +1,3 @@
# flake8: noqa: F401
from .VerifyCsrfToken import VerifyCsrfToken
from .AuthenticationMiddleware import AuthenticationMiddleware

12
myapp/app/models/User.py Normal file
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@ -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"

12
myapp/app/providers/AppProvider.py Normal file
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@ -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

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myapp/app/providers/__init__.py Normal file
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@ -0,0 +1,2 @@
# flake8: noqa: F401
from .AppProvider import AppProvider

0
myapp/config/__init__.py Normal file
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15
myapp/config/api.py Normal file
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@ -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,
}
}

16
myapp/config/application.py Normal file
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@ -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)

8
myapp/config/auth.py Normal file
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@ -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
}

14
myapp/config/broadcast.py Normal file
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@ -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,
},
}

25
myapp/config/cache.py Normal file
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@ -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",
},
}

56
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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)

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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"]
}
},
}

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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": "/",
}

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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,
},
}

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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

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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,
]

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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,
},
}

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# from masonite.environment import env
DRIVERS = {
"default": "cookie",
"cookie": {},
}

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#!/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()

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myapp/databases/migrations/2021_01_09_033202_create_password_reset_table.py Normal file
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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")

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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")

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"""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)

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"""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",
}
)

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init:
pip install -r requirements.txt
lint:
python -m flake8 .
format:
black .
make lint
serve:
python craft serve

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{
"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"
}
}

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[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",
]

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masonite>=4.0,<5.0
masonite-orm>=2.0,<3.0

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/* Put your CSS here */

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require("./bootstrap.js")

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/**
* 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');
}

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# routes/api.py
from masonite.routes import Route
ROUTES = [
Route.get('/users', 'UsersController@index')
]

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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")

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[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

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User-agent: *
Disallow:

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myapp/templates/__init__.py Normal file
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<meta name="csrf-token" content="{{ csrf_token }}">
<title>{% block title %}Masonite 4{% endblock %}</title>
<link rel="shortcut icon" href="/favicon.ico">
<link
href="https://unpkg.com/tailwindcss@^2/dist/tailwind.min.css"
rel="stylesheet"
/>
{% block head %}
<!-- <link rel="stylesheet" href="/assets/css/app.css"> -->
{% endblock %}
</head>
<body>
{% block content %}{% endblock %}
{% block js %}
<!-- <script src="/assets/js/app.js"></script> -->
{% endblock %}
</body>
</html>

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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<meta name="csrf-token" content="{{ csrf_token }}">
<title>{% block title %}Masonite 4{% endblock %}</title>
<link rel="shortcut icon" href="/favicon.ico">
<!-- CSS only -->
<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-1BmE4kWBq78iYhFldvKuhfTAU6auU8tT94WrHftjDbrCEXSU1oBoqyl2QvZ6jIW3" crossorigin="anonymous">
{% block head %}
<!-- <link rel="stylesheet" href="/assets/css/app.css"> -->
{% endblock %}
</head>
<body>
{% block content %}{% endblock %}
<!-- JavaScript Bundle with Popper -->
<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/js/bootstrap.bundle.min.js" integrity="sha384-ka7Sk0Gln4gmtz2MlQnikT1wXgYsOg+OMhuP+IlRH9sENBO0LRn5q+8nbTov4+1p" crossorigin="anonymous"></script>
{% block js %}
<!-- <script src="/assets/js/app.js"></script> -->
{% endblock %}
</body>
</html>

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This is a blog

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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Permission Denied</title>
<link href="https://unpkg.com/tailwindcss@^2/dist/tailwind.min.css" rel="stylesheet">
</head>
<body>
{% block content %}
<div class="h-screen flex flex-col items-center text-center justify-center">
<p class="text-center">Oops looks like you don't have access to this page !</p>
</div>
{% endblock %}
</body>
</html>

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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Page Not Found</title>
<link href="https://unpkg.com/tailwindcss@^2/dist/tailwind.min.css" rel="stylesheet">
</head>
<body>
{% block content %}
<div class="h-screen flex flex-col items-center text-center justify-center">
<p class="text-center">Oops this page does not exist !</p>
</div>
{% endblock %}
</body>
</html>

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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Error 500</title>
<link href="https://unpkg.com/tailwindcss@^2/dist/tailwind.min.css" rel="stylesheet">
</head>
<body>
{% block content %}
<div class="h-screen flex flex-col items-center text-center justify-center">
<p class="text-center">Oops an error happened !</p>
</div>
{% endblock %}
</body>
</html>

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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Server Maintenance</title>
<link href="https://unpkg.com/tailwindcss@^2/dist/tailwind.min.css" rel="stylesheet">
</head>
<body>
{% block content %}
<div class="h-screen flex flex-col items-center justify-center">
<p class="text-center">Sorry, this site is currently down for maintenance.</p>
</div>
{% endblock %}
</body>
</html>

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@extends 'base.html'
@block content
<form action="/patient/move" method="POST">
{{ csrf_field }}
<div class="mb-3">
<label for="MRN" class="form-label">病歷號</label>
<input type="text" class="form-control" id="MRN" aria-describedby="MRNHelp">
<div id="MRNHelp" class="form-text">Medical record number</div>
</div>
<button type="submit" class="btn btn-primary">Submit</button>
</form>
@endblock

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{% extends "base.html" %}
{% block title %}Welcome on Masonite 4{% endblock %}
{% block content %}
<div class="h-screen flex flex-col items-center justify-center">
<img src="/logo.png" alt="Masonite Logo" class="h-16 w-16 mb-4">
<div class="text-gray-500 text-5xl mb-10 tracking-wide">
Masonite 4
</div>
<nav class="flex space-x-4 justify-center text-gray-500 uppercase text-sm">
<a href="https://docs.masoniteproject.com" class="px-3 py-2 hover:text-indigo-700">
Documentation
</a>
<a href="https://discord.gg/HEQBAbTXt2" class="px-3 py-2 hover:text-indigo-700">
Join Discord Community
</a>
<a href="https://github.com/MasoniteFramework/masonite" class="px-3 py-2 hover:text-indigo-700">
GitHub
</a>
<a href="https://github.com/sponsors/MasoniteFramework" class="px-3 py-2 hover:text-indigo-700">
Sponsor us
</a>
<a href="https://twitter.com/masoniteproject" class="px-3 py-2 hover:text-indigo-700">
Follow us on Twitter
</a>
</nav>
</div>
{% endblock %}

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from masonite.tests import TestCase
class TestCase(TestCase):
def setUp(self):
super().setUp()

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from .TestCase import TestCase

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