Renamed folder due to conflicts, started work on

algorithm conformance
OSIPI · Aug 2, 2023 · aae8cc0 · aae8cc0
1 parent f13fc11
commit aae8cc0
Show file tree

Hide file tree

Showing 23 changed files with 51 additions and 9 deletions.
diff --git a/src/__pycache__/__init__.cpython-39.pyc b/src/__pycache__/__init__.cpython-39.pyc
diff --git a/src/original/ETP_SRI/LinearFitting.py b/src/original/ETP_SRI/LinearFitting.py
@@ -1,9 +1,7 @@
 import numpy as np
 import numpy.polynomial.polynomial as poly
 
-from utils.data_simulation.GenerateData import GenerateData
-
-
+from utilities.data_simulation.GenerateData import GenerateData
 
 class LinearFit:
     """

diff --git a/src/original/ETP_SRI/__pycache__/LinearFitting.cpython-39.pyc b/src/original/ETP_SRI/__pycache__/LinearFitting.cpython-39.pyc
diff --git a/src/original/ETP_SRI/__pycache__/__init__.cpython-39.pyc b/src/original/ETP_SRI/__pycache__/__init__.cpython-39.pyc
diff --git a/src/original/__pycache__/__init__.cpython-39.pyc b/src/original/__pycache__/__init__.cpython-39.pyc
diff --git a/src/standardized/ETP_SRI_LinearFitting.py b/src/standardized/ETP_SRI_LinearFitting.py
@@ -0,0 +1,32 @@
+import numpy as np
+from src.wrappers.OsipiBase import OsipiBase
+from src.original.ETP_SRI.LinearFitting import LinearFit
+
+
+class ETP_SRI_LinearFitting(OsipiBase):
+    """WIP
+    Implementation and execution of the submitted algorithm
+    """
+
+    def ivim_fit(self, signals, b_bvalues):
+        ETP_object = LinearFit(self.thresholds[0])
+
+        f, D, Dstar = ETP_object.ivim_fit(b_values, signals)
+
+
+
+        return (f, Dstar, D)
+
+
+
+# Simple test code... 
+b_values = np.array([0, 200, 500, 800])
+
+def ivim_model(b, S0=1, f=0.1, Dstar=0.03, D=0.001):
+    return S0*(f*np.exp(-b*Dstar) + (1-f)*np.exp(-b*D))
+
+signals = ivim_model(b_values)
+
+model = ETP_SRI_LinearFitting()
+model.thresholds = [200]
+results = model.ivim_fit(b_values, signals)
diff --git a/utils/__init__.py → src/standardized/__init__.py b/utils/__init__.py → src/standardized/__init__.py
diff --git a/src/wrappers/OsipiBase.py b/src/wrappers/OsipiBase.py
@@ -1,13 +1,17 @@
 
 
 
-class ivim_fit_osipi:
+class OsipiBase:
     """The base class for OSIPI IVIM fitting"""
+
+    #def __init__(self, author, data_dimension, thresholds_required, guess_required, bounds_required):
+    #    pass
 
-    def fit_osipi(self, data=None, bvalues=None, initial_guess=None, bounds=None, **kwargs):
+    def fit_osipi(self, data=None, b_values=None, initial_guess=None, bounds=None, **kwargs):
         """Fits the data with the bvalues
-        Returns [S0, f, D, D*]
+        Returns [S0, f, D*, D]
         """
+        #self.parameter_estimates = self.ivim_fit(data, b_values)
         pass
 
     def accepted_dimensions_osipi(self):
@@ -24,6 +28,10 @@ def accepts_dimension_osipi(self, dim):
         if dim < 0 or dim > len(accepted):
             return False
         return accepted[dim]
+
+    def thresholds_required_osipi():
+        """How many segmentation thresholds does it require?"""
+        return 0
 
     def guess_required_osipi():
         """Does it require an initial guess?"""
@@ -36,3 +44,7 @@ def bounds_required_osipi():
     def author_osipi():
         """Author identification"""
         return ''
+
+    def simple_test():
+        pass
+
diff --git a/src/wrappers/__init__.py b/src/wrappers/__init__.py
diff --git a/src/wrappers/__pycache__/OsipiBase.cpython-39.pyc b/src/wrappers/__pycache__/OsipiBase.cpython-39.pyc
diff --git a/src/wrappers/__pycache__/__init__.cpython-39.pyc b/src/wrappers/__pycache__/__init__.cpython-39.pyc
diff --git a/tests/IVIMmodels/data/test_GenerateData.py b/tests/IVIMmodels/data/test_GenerateData.py
@@ -3,7 +3,7 @@
 import pytest
 import torch
 
-from utils.data_simulation.GenerateData import GenerateData
+from utilities.data_simulation.GenerateData import GenerateData
 
 #run using python -m pytest from the root folder
 

diff --git a/tests/IVIMmodels/unit_tests/test_ivim_fit_linear.py b/tests/IVIMmodels/unit_tests/test_ivim_fit_linear.py
@@ -3,7 +3,7 @@
 import pytest
 import torch
 
-from utils.data_simulation.GenerateData import GenerateData
+from utilities.data_simulation.GenerateData import GenerateData
 from src.original.ETP_SRI.LinearFitting import LinearFit
 
 

diff --git a/utilities/__init__.py b/utilities/__init__.py
diff --git a/utilities/__pycache__/__init__.cpython-39.pyc b/utilities/__pycache__/__init__.cpython-39.pyc
diff --git a/utils/data_simulation/GenerateData.py → utilities/data_simulation/GenerateData.py b/utils/data_simulation/GenerateData.py → utilities/data_simulation/GenerateData.py
diff --git a/utilities/data_simulation/__init__.py b/utilities/data_simulation/__init__.py
diff --git a/utilities/data_simulation/__pycache__/GenerateData.cpython-39.pyc b/utilities/data_simulation/__pycache__/GenerateData.cpython-39.pyc
diff --git a/utilities/data_simulation/__pycache__/__init__.cpython-39.pyc b/utilities/data_simulation/__pycache__/__init__.cpython-39.pyc
diff --git a/utils/data_simulation/ivim_simulation.py → utilities/data_simulation/ivim_simulation.py b/utils/data_simulation/ivim_simulation.py → utilities/data_simulation/ivim_simulation.py
@@ -1,7 +1,7 @@
 import torch
 import numpy as np
 
-from utils.ivim.forward_model import ivim_parameters_to_signal
+from utilities.ivim.forward_model import ivim_parameters_to_signal
 
 
 def simulate_ivim_signal(D, Dp, f, S0, bvalues, SNR_array, rg):

diff --git a/utils/digital_reference_object/DRO.npy → utilities/digital_reference_object/DRO.npy b/utils/digital_reference_object/DRO.npy → utilities/digital_reference_object/DRO.npy
diff --git a/...igital_reference_object/howto_load_dro.md → ...igital_reference_object/howto_load_dro.md b/...igital_reference_object/howto_load_dro.md → ...igital_reference_object/howto_load_dro.md
diff --git a/utils/ivim/forward_model.py → utilities/ivim/forward_model.py b/utils/ivim/forward_model.py → utilities/ivim/forward_model.py