Matlab installation + adding Amita's code to wrapper

.gitignore

@@ -19,8 +19,10 @@ md5sums.txt
 *.asv
 src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/test_data
 src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/output_files
-
-
+tests/IVIMmodels/unit_tests/*.log
+junit/*
+ivim_simulation.bval
+ivim_simulation.bvec
 
 # Unit test / coverage reports
 .tox/

conftest.py

@@ -81,6 +81,24 @@ def pytest_addoption(parser):
         type=str,
         help="Drop this algorithm from the list"
     )
+    parser.addoption(
+        "--withmatlab",
+        action="store_true",
+        default=False,
+        help="Run MATLAB-dependent tests"
+    )
+
+
+@pytest.fixture(scope="session")
+def eng(request):
+    """Start and return a MATLAB engine session if --withmatlab is set."""
+    if not request.config.getoption("--withmatlab"):
+        return None
+    import matlab.engine
+    print("Starting MATLAB engine...")
+    eng = matlab.engine.start_matlab()
+    print("MATLAB engine started.")
+    return eng
 
 
 @pytest.fixture(scope="session")
@@ -149,25 +167,20 @@ def use_prior(request):
 def pytest_generate_tests(metafunc):
     if "SNR" in metafunc.fixturenames:
         metafunc.parametrize("SNR", metafunc.config.getoption("SNR"))
-    if "ivim_algorithm" in metafunc.fixturenames:
-        algorithms = algorithm_list(metafunc.config.getoption("algorithmFile"), metafunc.config.getoption("selectAlgorithm"), metafunc.config.getoption("dropAlgorithm"))
-        metafunc.parametrize("ivim_algorithm", algorithms)
     if "ivim_data" in metafunc.fixturenames:
         data = data_list(metafunc.config.getoption("dataFile"))
         metafunc.parametrize("ivim_data", data)
+    if "data_ivim_fit_saved" in  metafunc.fixturenames:
+        args = data_ivim_fit_saved(metafunc.config.getoption("dataFile"),metafunc.config.getoption("algorithmFile"))
+        metafunc.parametrize("data_ivim_fit_saved", args)
+    if "algorithmlist" in metafunc.fixturenames:
+        args = algorithmlist(metafunc.config.getoption("algorithmFile"))
+        metafunc.parametrize("algorithmlist", args)
+    if "bound_input" in metafunc.fixturenames:
+        args = bound_input(metafunc.config.getoption("dataFile"),metafunc.config.getoption("algorithmFile"))
+        metafunc.parametrize("bound_input", args)
 
 
-def algorithm_list(filename, selected, dropped):
-    current_folder = pathlib.Path.cwd()
-    algorithm_path = current_folder / filename
-    with algorithm_path.open() as f:
-        algorithm_information = json.load(f)
-    algorithms = set(algorithm_information["algorithms"])
-    algorithms = algorithms - set(dropped)
-    if len(selected) > 0 and selected[0]:
-        algorithms = algorithms & set(selected)
-    return list(algorithms)
-
 def data_list(filename):
     current_folder = pathlib.Path.cwd()
     data_path = current_folder / filename
@@ -178,3 +191,69 @@ def data_list(filename):
     bvals = bvals['bvalues']
     for name, data in all_data.items():
         yield name, bvals, data
+
+
+def data_ivim_fit_saved(datafile, algorithmFile):
+    # Find the algorithms from algorithms.json
+    current_folder = pathlib.Path.cwd()
+    algorithm_path = current_folder / algorithmFile
+    with algorithm_path.open() as f:
+        algorithm_information = json.load(f)
+    # Load generic test data generated from the included phantom: phantoms/MR_XCAT_qMRI
+    generic = current_folder / datafile
+    with generic.open() as f:
+        all_data = json.load(f)
+    algorithms = algorithm_information["algorithms"]
+    bvals = all_data.pop('config')
+    bvals = bvals['bvalues']
+    for algorithm in algorithms:
+        first = True
+        for name, data in all_data.items():
+            algorithm_dict = algorithm_information.get(algorithm, {})
+            xfail = {"xfail": name in algorithm_dict.get("xfail_names", {}),
+                "strict": algorithm_dict.get("xfail_names", {}).get(name, True)}
+            kwargs = algorithm_dict.get("options", {})
+            tolerances = algorithm_dict.get("tolerances", {})
+            skiptime=False
+            if first:
+                if algorithm_dict.get("fail_first_time", False):
+                    skiptime = True
+                    first = False
+            requires_matlab = algorithm_dict.get("requires_matlab", False)
+            yield name, bvals, data, algorithm, xfail, kwargs, tolerances, skiptime, requires_matlab
+
+def algorithmlist(algorithmFile):
+    # Find the algorithms from algorithms.json
+    current_folder = pathlib.Path.cwd()
+    algorithm_path = current_folder / algorithmFile
+    with algorithm_path.open() as f:
+        algorithm_information = json.load(f)
+
+    algorithms = algorithm_information["algorithms"]
+    for algorithm in algorithms:
+        algorithm_dict = algorithm_information.get(algorithm, {})
+        requires_matlab = algorithm_dict.get("requires_matlab", False)
+        yield algorithm, requires_matlab
+
+def bound_input(datafile,algorithmFile):
+    # Find the algorithms from algorithms.json
+    current_folder = pathlib.Path.cwd()
+    algorithm_path = current_folder / algorithmFile
+    with algorithm_path.open() as f:
+        algorithm_information = json.load(f)
+    # Load generic test data generated from the included phantom: phantoms/MR_XCAT_qMRI
+    generic = current_folder / datafile
+    with generic.open() as f:
+        all_data = json.load(f)
+    algorithms = algorithm_information["algorithms"]
+    bvals = all_data.pop('config')
+    bvals = bvals['bvalues']
+    for name, data in all_data.items():
+        for algorithm in algorithms:
+            algorithm_dict = algorithm_information.get(algorithm, {})
+            xfail = {"xfail": name in algorithm_dict.get("xfail_names", {}),
+                "strict": algorithm_dict.get("xfail_names", {}).get(name, True)}
+            kwargs = algorithm_dict.get("options", {})
+            tolerances = algorithm_dict.get("tolerances", {})
+            requires_matlab = algorithm_dict.get("requires_matlab", False)
+            yield name, bvals, data, algorithm, xfail, kwargs, tolerances, requires_matlab

pytest.ini

@@ -2,4 +2,5 @@
 markers =
     slow: marks tests as slow (deselect with '-m "not slow"')
 addopts =  
-    -m 'not slow'
+    -m 'not slow'
+testpaths = tests

src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py

@@ -0,0 +1,120 @@
+from src.wrappers.OsipiBase import OsipiBase
+import numpy as np
+import matlab.engine
+
+
+class ASD_MemorialSloanKettering_QAMPER_IVIM(OsipiBase):
+    """
+    Bi-exponential fitting algorithm by Oliver Gurney-Champion, Amsterdam UMC
+    """
+
+    # I'm thinking that we define default attributes for each submission like this
+    # And in __init__, we can call the OsipiBase control functions to check whether
+    # the user inputs fulfil the requirements
+
+    # Some basic stuff that identifies the algorithm
+    id_author = "LoCastro, Dr. Ramesh Paudyal, Dr. Amita Shukla-Dave"
+    id_algorithm_type = "Bi-exponential fit"
+    id_return_parameters = "f, D*, D, S0"
+    id_units = "seconds per milli metre squared or milliseconds per micro metre squared"
+
+    # Algorithm requirements
+    required_bvalues = 4
+    required_thresholds = [0,
+                           0]  # Interval from "at least" to "at most", in case submissions allow a custom number of thresholds
+    required_bounds = False
+    required_bounds_optional = True  # Bounds may not be required but are optional
+    required_initial_guess = False
+    required_initial_guess_optional = True
+    accepted_dimensions = 1  # Not sure how to define this for the number of accepted dimensions. Perhaps like the thresholds, at least and at most?
+
+    # Supported inputs in the standardized class
+    supported_bounds = True
+    supported_initial_guess = True
+    supported_thresholds = False
+
+    def __init__(self, bvalues=None, thresholds=None, bounds=None, initial_guess=None, eng=None):
+        """
+            Everything this algorithm requires should be implemented here.
+            Number of segmentation thresholds, bounds, etc.
+
+            Our OsipiBase object could contain functions that compare the inputs with
+            the requirements.
+        """
+        #super(OGC_AmsterdamUMC_biexp, self).__init__(bvalues, bounds, initial_guess, fitS0)
+        super(ASD_MemorialSloanKettering_QAMPER_IVIM, self).__init__(bvalues=bvalues, bounds=bounds, initial_guess=initial_guess)
+        self.initialize(bounds, initial_guess)
+        if eng is None:
+            print('initiating matlab; this may take some time. For repeated testing one could use the optional input eng as an already initiated matlab engine')
+            self.eng=matlab.engine.start_matlab()
+            self.keep_alive=False
+        else:
+            self.eng = eng
+            self.keep_alive=True
+
+    def algorithm(self,dwi_arr, bval_arr, LB0, UB0, x0in):
+        dwi_arr = matlab.double(dwi_arr.tolist())
+        bval_arr = matlab.double(bval_arr.tolist())
+        LB0 = matlab.double(LB0.tolist())
+        UB0 = matlab.double(UB0.tolist())
+        x0in = matlab.double(x0in.tolist())
+        results = self.eng.IVIM_standard_bcin(
+            dwi_arr, bval_arr, 0.0, LB0, UB0, x0in, False, 0, 0,nargout=11)
+        (f_arr, D_arr, Dx_arr, s0_arr, fitted_dwi_arr, RSS, rms_val, chi, AIC, BIC, R_sq) = results
+        return D_arr/1000, f_arr, Dx_arr/1000, s0_arr
+
+    def initialize(self, bounds, initial_guess):
+        if bounds is None:
+            print('warning, no bounds were defined, so algorithm-specific default bounds are used')
+            self.bounds=([1e-6, 0, 0.004, 0],[0.003, 1.0, 0.2, 5])
+        else:
+            self.bounds=bounds
+        if initial_guess is None:
+            print('warning, no initial guesses were defined, so algorithm-specific default initial guess is used')
+            self.initial_guess = [0.001, 0.2, 0.01, 1]
+        else:
+            self.initial_guess = initial_guess
+            self.use_initial_guess = True
+        self.use_initial_guess = True
+        self.use_bounds = True
+
+    def ivim_fit(self, signals, bvalues, **kwargs):
+        """Perform the IVIM fit
+
+        Args:
+            signals (array-like)
+            bvalues (array-like, optional): b-values for the signals. If None, self.bvalues will be used. Default is None.
+
+        Returns:
+            _type_: _description_
+        """
+
+        bvalues=np.array(bvalues)
+        LB = np.array(self.bounds[0])[[1,0,2,3]]
+        UB = np.array(self.bounds[1])[[1,0,2,3]]
+
+        fit_results = self.algorithm(np.array(signals)[:,np.newaxis], bvalues, LB, UB, np.array(self.initial_guess)[[1,0,2,3]])
+
+        results = {}
+        results["D"] = fit_results[0]
+        results["f"] = fit_results[1]
+        results["Dp"] = fit_results[2]
+
+        return results
+
+    def clean(self):
+        if not self.keep_alive:
+            if hasattr(self, "eng") and self.eng:
+                try:
+                    self.eng.quit()
+                except Exception as e:
+                    print(f"Warning: Failed to quit MATLAB engine cleanly: {e}")
+
+    def __del__(self):
+        self.clean()
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        self.clean()

src/standardized/OGC_AmsterdamUMC_biexp.py

@@ -55,7 +55,7 @@ def initialize(self, bounds, initial_guess, fitS0):
             self.bounds=bounds
         if initial_guess is None:
             print('warning, no initial guesses were defined, so default bounds are used of  [0.001, 0.001, 0.01, 1]')
-            self.initial_guess = [0.001, 0.001, 0.01, 1]
+            self.initial_guess = [0.001, 0.1, 0.01, 1]
         else:
             self.initial_guess = initial_guess
             self.use_initial_guess = True

tests/IVIMmodels/unit_tests/algorithms.json

@@ -1,5 +1,6 @@
 {
     "algorithms": [
+        "ASD_MemorialSloanKettering_QAMPER_IVIM",
         "ETP_SRI_LinearFitting",
         "IAR_LU_biexp",
         "IAR_LU_modified_mix",
@@ -14,6 +15,9 @@
         "PvH_KB_NKI_IVIMfit",
         "OJ_GU_seg"
     ],
+    "ASD_MemorialSloanKettering_QAMPER_IVIM": {
+        "requires_matlab": true
+    },
     "IAR_LU_biexp": {
         "fail_first_time": true
     },