add range shifter support

README.md

@@ -4,10 +4,10 @@ Script for manipulating dicom plans
 
 ```
 $ python3 dicomfix/main.py -h
-usage: main.py [-h] [-w WEIGHTS] [-o OUTPUT] [-e EXPORT_RACEHORSE] [-a] [-dt] [-ic] [-i] [-tr4] [-rs] [-p PRINT_SPOTS]
-               [-g GANTRY_ANGLES] [-d DUPLICATE_FIELDS] [-rd RESCALE_DOSE] [-rf RESCALE_FACTOR] [-rm] [-tp TABLE_POSITION]
-               [-sp SNOUT_POSITION] [-tm TREATMENT_MACHINE] [-pl PLAN_LABEL] [-pn PATIENT_NAME] [-rn REVIEWER_NAME] [-v] [-V]
-               [inputfile]
+usage: main.py [-h] [-w WEIGHTS] [-o OUTPUT] [-e EXPORT_RACEHORSE] [-a] [-dt] [-ic] [-i] [-ia] [-tr4] [-rs]
+               [-p PRINT_SPOTS] [-g GANTRY_ANGLES] [-d DUPLICATE_FIELDS] [-rd RESCALE_DOSE] [-rf RESCALE_FACTOR]
+               [-rm] [-tp TABLE_POSITION] [-sp SNOUT_POSITION] [-tm TREATMENT_MACHINE] [-pl PLAN_LABEL]
+               [-pn PATIENT_NAME] [-rn REVIEWER_NAME] [-v] [-V] [inputfile]
 
 Modify ECLIPSE DICOM proton therapy treatment plans.
 
@@ -26,7 +26,8 @@ options:
   -dt, --date           Set RT date to now
   -ic, --intent_curative
                         Set plan intent to CURATIVE
-  -i, --inspect         Print contents of DICOM file and exit
+  -i, --inspect         Print a summary of the DICOM file and exit
+  -ia, --inspect_all    Print all tags in the DICOM file and exit
   -tr4, --wizard_tr4    Prepare plan for TR4: sets approval, gantry, snout, and treatment machine
   -rs, --fix_raystation
                         Make RayStation plans compatible with Varian proton systems
@@ -57,3 +58,10 @@ options:
   -v, --verbosity       Give more output. Option is additive, can be used up to 3 times
   -V, --version         show program's version number and exit
 ```
+
+
+To run locally in venv
+```
+~/Projects/dicomfix$ pip install -e .
+~/Projects/dicomfix$ python dicomfix/main.py
+```

dicomfix/__version__.py

@@ -1,3 +1,6 @@
-from importlib.metadata import version as get_version
+from importlib.metadata import version, PackageNotFoundError
 
-__version__ = get_version("dicomfix")
+try:
+    __version__ = version("dicomfix")
+except PackageNotFoundError:
+    __version__ = "0.0.0"  # Fallback version if package metadata is unavailable

dicomfix/config.py

@@ -22,6 +22,7 @@ def __init__(self, parsed_args):
         self.date = parsed_args.date
         self.intent_curative = parsed_args.intent_curative
         self.inspect = parsed_args.inspect
+        self.inspect_all = parsed_args.inspect_all
         self.wizard_tr4 = parsed_args.wizard_tr4
         self.fix_raystation = parsed_args.fix_raystation
         self.print_spots = parsed_args.print_spots

dicomfix/config_parser.py

@@ -30,7 +30,10 @@ def parse_arguments(args=None):
     parser.add_argument('-dt', '--date', action='store_true', default=False, help='Set RT date to now')
     parser.add_argument('-ic', '--intent_curative', action='store_true', default=False,
                         help='Set plan intent to CURATIVE')
-    parser.add_argument('-i', '--inspect', action='store_true', default=False, help='Print contents of DICOM file and exit')
+    parser.add_argument('-i', '--inspect', action='store_true', default=False,
+                        help='Print a summary of the DICOM file and exit')
+    parser.add_argument('-ia', '--inspect_all', action='store_true', default=False,
+                        help='Print all tags in the DICOM file and exit')
     parser.add_argument('-tr4', '--wizard_tr4', action='store_true', default=False,
                         help='Prepare plan for TR4: sets approval, gantry, snout, and treatment machine')
 

dicomfix/dicomutil.py

@@ -52,9 +52,11 @@ def __init__(self, inputfile):
         self.old_dicom = copy.deepcopy(self.dicom)
         self.spots_discarded = 0  # count of spots discarded due to low MU
         self.total_number_of_spots = 0
-        for ib in self.dicom.IonBeamSequence:
-            self.total_number_of_spots += sum([icp.NumberOfScanSpotPositions for icp in ib.IonControlPointSequence])
-        self.total_number_of_spots = self.total_number_of_spots // 2  # divide by 2, as each spot has two control points
+
+        if hasattr(self.dicom, "IonBeamSequence"):
+            for ib in self.dicom.IonBeamSequence:
+                self.total_number_of_spots += sum([icp.NumberOfScanSpotPositions for icp in ib.IonControlPointSequence])
+            self.total_number_of_spots = self.total_number_of_spots // 2  # divide by 2, as each spot has two control points
 
     @staticmethod
     def load_dicom(inputfile):
@@ -716,6 +718,12 @@ def safe_get(attr, default="N/A"):
         # Return the concatenated output as a string
         return "\n".join(output)
 
+    def inspect_all(self):
+        """ Print all attributes of the DICOM file to the console. """
+
+        logger.debug("Inspecting all DICOM attributes:")
+        print(self.dicom)
+
     def print_dicom_spot_comparison(self, num_values):
         """
         Compare spot meterset weights between the original and modified DICOM plans.

dicomfix/main.py

@@ -48,7 +48,12 @@ def main(args=None):
 
     # Handle inspect option
     if config.inspect:
-        logger.info(dp.inspect())
+        print(dp.inspect())
+        exit(0)
+
+    # Handle inspect_all option
+    if config.inspect_all:
+        print(dp.inspect_all())
         exit(0)
 
     # Apply all modifications to the plan using the config object

docker/Dockerfile

@@ -12,13 +12,17 @@ RUN pip install --upgrade pip \
     && pip install .
 
 # Install optional dependencies for web UI (Streamlit)
-RUN pip install .[dev]
-RUN pip install .[web]
+RUN pip install .[dev,web]
 
 RUN pytest tests/
 
+# Command to run the Streamlit app
+# http
 # Expose the port that Streamlit will run on
-EXPOSE 8501
+# EXPOSE 8501
+# CMD ["streamlit", "run", "dicomfix/web/app.py", "--server.port=8501", "--server.address=0.0.0.0"]
+
+# https if you have the certificate and key files
+EXPOSE 8443
+CMD ["streamlit", "run", "dicomfix/web/app.py", "--server.port=8443", "--server.address=0.0.0.0", "--server.sslCertFile=${SSL_CERT_FILE}", "--server.sslKeyFile=${SSL_KEY_FILE}"]
 
-# Command to run the Streamlit app
-CMD ["streamlit", "run", "dicomfix/web/app.py", "--server.port=8501", "--server.address=0.0.0.0"]

docker/README.md

@@ -1,15 +1,20 @@
 ```
-docker build -t dicomfix-webapp -f docker/Dockerfile .
-docker run -p 8501:8501 dicomfix-webapp
+sudo docker build -t dicomfix-webapp -f docker/Dockerfile .
+sudo docker run -p 8501:8501 dicomfix-webapp
 ```
 To export to systems with no www access
 ```
-docker save -o dicomfix-webapp.tar dicomfix-webapp
+sudo docker save -o dicomfix-webapp.tar dicomfix-webapp
+sudo chown xxx:xxx dicomfix-webapp.tar
 scp dicomfix-webapp.tar xxx@xxx:/xxx
 ```
 
 On remote system:
 ```
 docker load -i ./dicomfix-webapp.tar
-docker run -p 8501:8501 dicomfix-webapp
+# HTTP version:
+docker run -p 8501:8501 dicomfix-webapp  # will overwrite any existing :latest image
+
+# HTTPS version:
+docker run -p 8443:8443 -e SSL_CERT_FILE=/etc/ssl/certs/dicomfix.crt -e SSL_KEY_FILE=/etc/ssl/private/dicomfix.key dicomfix-webapp:latest
 ```

docker/dicomfix-webapp.service

@@ -0,0 +1,22 @@
+[Unit]
+Description=DicomFix WebApp Docker Container
+After=network.target
+
+[Service]
+User=dcptclin
+Restart=always
+# ExecStart=/usr/bin/docker run --privileged -p 8501:8501 dicomfix-webapp  # http
+xecStart=/usr/bin/docker run --privileged \
+  -p 8443:8443 \
+  -e SSL_CERT_FILE=/etc/ssl/certs/dicomfix.crt \
+  -e SSL_KEY_FILE=/etc/ssl/private/dicomfix.key \
+  -v /etc/ssl/certs/dicomfix.crt:/etc/ssl/certs/dicomfix.crt:ro \
+  -v /etc/ssl/private/dicomfix.key:/etc/ssl/private/dicomfix.key:ro \
+  dicomfix-webapp:latest
+ExecStop=/usr/bin/docker stop dicomfix-webapp
+ExecStopPost=/usr/bin/docker rm dicomfix-webapp
+TimeoutSec=30
+RestartSec=10
+
+[Install]
+WantedBy=multi-user.target

pyproject.toml

@@ -1,6 +1,10 @@
+[build-system]
+requires = ["setuptools>=42", "wheel", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
 [project]
 name = "dicomfix"
-version = "0.1.0"
+# version = "0.1.0"  # Version is managed by setuptools_scm
 description = "A brief description of what your project does"
 authors = [
     { name = "Niels Bassler", email = "[email protected]" },
@@ -14,6 +18,7 @@ dependencies = [
     "pylibjpeg-openjpeg", # Support for JPEG 2000 compression
     "pillow",             # Support for other image formats
 ]
+dynamic = ["version"]
 
 [tool.setuptools]
 packages = ["dicomfix"]
@@ -41,5 +46,5 @@ based_on_style = "pep8"
 column_limit = 127
 
 [tool.setuptools_scm]
-version_scheme = "guess-next-dev"
-local_scheme = "node-and-timestamp"
+version_scheme = "post-release"
+local_scheme = "node-and-date"