Version 1.0.4.6: Make Mosek and pydicom optional dependency.

README.md

@@ -3,7 +3,7 @@
   <img src="./images/PortPy_logo.png" width="40%" height="40%">
 </p>
 
-![Version](https://img.shields.io/static/v1?label=latest&message=v1.0.4.5&color=darkgreen)
+![Version](https://img.shields.io/static/v1?label=latest&message=v1.0.4.6&color=darkgreen)
 [![Total Downloads](https://static.pepy.tech/personalized-badge/portpy?period=total&units=international_system&left_color=grey&right_color=blue&left_text=total%20downloads)](https://pepy.tech/project/portpy?&left_text=totalusers)
 [![Monthly Downloads](https://static.pepy.tech/badge/portpy/month)](https://pepy.tech/project/portpy)
 # What is PortPy?

portpy/__init__.py

@@ -1,3 +1,3 @@
-__version__ = "1.0.4.5"
+__version__ = "1.0.4.6"
 
 from portpy import photon

portpy/photon/optimization.py

@@ -343,7 +343,22 @@ def solve(self, return_cvxpy_prob=False, *args, **kwargs):
         problem = cp.Problem(cp.Minimize(cp.sum(self.obj)), constraints=self.constraints)
         print('Running Optimization..')
         t = time.time()
-        problem.solve(*args, **kwargs)
+        # Check if 'solver' is passed in args
+        solver = kwargs.get('solver', None)
+        if solver and solver.lower() == 'mosek':
+            try:
+                problem.solve(*args, **kwargs)  # Attempt to solve with mosek
+            except cp.error.SolverError as e:
+                # Raise a custom error if MOSEK is not installed or available
+                raise ImportError(
+                    "MOSEK solver is not installed. You can obtain the MOSEK license file by applying using an .edu account. \n"
+                    r"The license file should be placed in the directory C:\\Users\\username\\mosek."
+                    "\n To use MOSEK, install it using: pip install portpy[mosek].\n"
+                    "If a license is not available, you may try open-source or free solvers like SCS or ECOS. \n"
+                    "Please refer to the CVXPy documentation for more information about its various solvers.\n"
+                ) from e
+        else:
+            problem.solve(*args, **kwargs)  # Continue solving with other solvers
         elapsed = time.time() - t
         self.obj_value = problem.value
         print("Optimal value: %s" % problem.value)

portpy/photon/utils/convert_dose_rt_dicom_to_portpy.py

@@ -2,7 +2,11 @@
 from __future__ import annotations
 import os
 import SimpleITK as sitk
-from pydicom import dcmread
+try:
+    from pydicom import dcmread
+    pydicom_installed = True
+except ImportError:
+    pydicom_installed = False
 import numpy as np
 from portpy.photon.ct import CT
 from typing import TYPE_CHECKING
@@ -74,6 +78,10 @@ def get_ct_image(ct: CT):
 
 
 def convert_dose_rt_dicom_to_portpy(my_plan: Plan = None, ct: CT = None, dir_name: str = None, dose_file_name: str = None):
+    if not pydicom_installed:
+        raise ImportError(
+            "Pydicom. To use this function, please install it with `pip install portpy[pydicom]`."
+        )
     dicom_dose_image = read_dicom_dose(dir_name=dir_name, dose_file_name=dose_file_name)
     if ct is None:
         ct = my_plan.ct

portpy/photon/utils/write_rt_plan_imrt.py

@@ -2,8 +2,12 @@
 from typing import TYPE_CHECKING
 if TYPE_CHECKING:
     from portpy.photon.plan import Plan
-from pydicom import dcmread
-from pydicom import Dataset, Sequence
+try:
+    from pydicom import dcmread
+    from pydicom import Dataset, Sequence
+    pydicom_installed = True
+except ImportError:
+    pydicom_installed = False
 
 
 def write_rt_plan_imrt(my_plan: Plan, leaf_sequencing: dict, out_rt_plan_file: str, in_rt_plan_file: str):
@@ -23,6 +27,11 @@ def write_rt_plan_imrt(my_plan: Plan, leaf_sequencing: dict, out_rt_plan_file: s
     # bottom_right_y_mm = my_plan.beams.beams_dict['jaw_position'][0]['bottom_right_y_mm']
     # top_left_y_mm = my_plan.beams.beams_dict['jaw_position'][0]['top_left_y_mm']
 
+    if not pydicom_installed:
+        raise ImportError(
+            "Pydicom. To use this function, please install it with `pip install portpy[pydicom]`."
+        )
+
     # read rt plan file using pydicom
     ds = dcmread(in_rt_plan_file)
     for b in range(len(ds.BeamSequence)):

portpy/photon/utils/write_rt_plan_vmat.py

@@ -3,8 +3,12 @@
 if TYPE_CHECKING:
     from portpy.photon.plan import Plan
     from portpy.photon.beam import Beams
-from pydicom import dcmread
-from pydicom import Dataset, Sequence
+try:
+    from pydicom import dcmread
+    from pydicom import Dataset, Sequence
+    pydicom_installed = True
+except ImportError:
+    pydicom_installed = False
 import numpy as np
 
 
@@ -173,7 +177,10 @@ def write_rt_plan_vmat(my_plan: Plan, out_rt_plan_file: str, in_rt_plan_file: st
     :param out_rt_plan_file: new rt plan which can be imported in TPS
 
     """
-
+    if not pydicom_installed:
+        raise ImportError(
+            "Pydicom. To use this function, please install it with `pip install portpy[pydicom]`."
+        )
     # read rt plan file using pydicom
     ds = dcmread(in_rt_plan_file)
     del ds.BeamSequence

setup.py

@@ -50,7 +50,6 @@ def _get_portpy_photon_version():
         "cvxpy>=1.1.18",
         "ecos>=2.0.10",
         "h5py>=3.6.0",
-        "Mosek>=9.3.14",
         "natsort>=8.1.0",
         "numpy>=1.15",
         "osqp>=0.4.1",
@@ -70,7 +69,11 @@ def _get_portpy_photon_version():
         "typing-extensions>=3.10.0.0",
         "scikit-image>=0.17.2",
         "patchify>=0.2.3",
-        "pydicom>=2.2.0",
     ],
+    extras_require={
+        'mosek': ["Mosek>=9.3.14"],
+        'pydicom': ["pydicom>=2.2.0"],
+        'full': ["Mosek>=9.3.14", "pydicom>=2.2.0"]
+    }
 
 )