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oliverchampionoliverchampion
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Merge branch 'main' into Unit_Testing_Tolerances
2 parents ba9fa91 + c9af8ef commit 59767b5

24 files changed

+157
-220
lines changed

‎.github/workflows/analysis.yml‎

Lines changed: 12 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -70,20 +70,21 @@ jobs:
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run: |
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python -m pytest -m slow --selectAlgorithm ${{ matrix.algorithm }} --saveFileName test_output_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv --SNR ${{ matrix.SNR }} --fitCount 300 --saveDurationFileName test_duration_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv
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- name: Upload raw data
73-
uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: Working_Data
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retention-days: 1
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path: |
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test_output_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv
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test_duration_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv
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overwrite: true
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merge:
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runs-on: ubuntu-latest
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needs: build
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steps:
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- name: Download artifacts
86-
uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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path: artifacts
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- name: Merge fitting results
@@ -95,12 +96,13 @@ jobs:
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head -n 1 $(ls artifacts/Working_Data/test_duration_*.csv | head -n 1) > test_duration.csv
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tail -q -n +2 artifacts/Working_Data/test_duration_*.csv >> test_duration.csv
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- name: Upload merged artifacts
98-
uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: Data
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path: |
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test_output.csv
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test_duration.csv
105+
overwrite: true
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analyze:
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runs-on: ubuntu-latest
@@ -121,13 +123,13 @@ jobs:
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any::data.table
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any::ggplot2
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- name: Download artifacts
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: Data
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- name: Generate figures
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run: Rscript --vanilla tests/IVIMmodels/unit_tests/analyze.r test_output.csv test_duration.csv
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- name: Upload figures
130-
uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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if: always()
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with:
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name: Figures
@@ -141,6 +143,8 @@ jobs:
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durations.pdf
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curve_plot.pdf
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fitted_curves.pdf
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overwrite: true
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compare:
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runs-on: ubuntu-latest
@@ -158,16 +162,17 @@ jobs:
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any::tidyverse
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any::assertr
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- name: Download artifacts
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: Data
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- name: Test against previous results
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run: Rscript --vanilla tests/IVIMmodels/unit_tests/compare.r test_output.csv test_reference.csv tests/IVIMmodels/unit_tests/reference_output.csv test_results.csv
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- name: Upload data
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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if: always()
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with:
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name: Comparison
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path: |
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test_reference.csv
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test_results.csv
178+
overwrite: true

‎src/original/IAR_LundUniversity/ivim_fit_method_biexp.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -61,13 +61,13 @@ def ivim_model(self, b, S0, f, D_star, D):
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6262
def set_bounds(self, bounds):
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# Use this function for fits that uses curve_fit
64-
if bounds == None:
64+
if bounds is None:
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self.bounds = np.array([(0, 0, 0.005, 0), (np.inf, 1, 0.1, 0.004)])
6666
else:
67-
self.bounds = np.array([(0, *bounds[0]), (np.inf, *bounds[1])])
67+
self.bounds = np.array([bounds[0], bounds[1]])
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6969
def set_initial_guess(self, initial_guess):
70-
if initial_guess == None:
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if initial_guess is None:
7171
self.initial_guess = (1, 0.2, 0.03, 0.001)
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else:
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self.initial_guess = initial_guess

‎src/original/IAR_LundUniversity/ivim_fit_method_linear.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -83,13 +83,13 @@ def sivim_model(self, b, S0, f, D):
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def set_bounds(self, bounds):
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# Use this function for fits that uses curve_fit
86-
if bounds == None:
86+
if bounds is None:
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self.bounds = np.array([(0, 0, 0), (np.inf, 1, 0.004)])
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else:
89-
self.bounds = np.array([(0, *bounds[0]), (np.inf, *bounds[1])])
89+
self.bounds = np.array([bounds[0], bounds[1]])
9090

9191
def set_initial_guess(self, initial_guess):
92-
if initial_guess == None:
92+
if initial_guess is None:
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self.initial_guess = (1, 0.2, 0.001)
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else:
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self.initial_guess = initial_guess

‎src/original/IAR_LundUniversity/ivim_fit_method_modified_mix.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -78,7 +78,7 @@ def __init__(self, gtab, bounds=None, maxiter=10, xtol=1e-8, rescale_units=False
7878
if gtab.bvals[-1] >= 10:
7979
self.bvals = gtab.bvals/1000
8080

81-
if bounds == None:
81+
if bounds is None:
8282
# Bounds expressed as (lower bound, upper bound) for [f, D*, D].
8383
self.bounds = np.array([(0, 1), (5, 100), (0, 4)])
8484
elif (bounds[0][1] <= 1) or rescale_units: # Realistically, if mm2/s units are used, D* bound is <= 1

‎src/original/IAR_LundUniversity/ivim_fit_method_modified_topopro.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -76,7 +76,7 @@ def __init__(self, gtab, bounds=[[0, 0.005, 1e-5], [1, 0.1, 0.004]], \
7676
# and are thus not changed.
7777
if gtab.bvals[-1] >= 10:
7878
self.bvals = gtab.bvals/1000
79-
if bounds == None:
79+
if bounds is None:
8080
# Bounds expressed as (lower bound, upper bound) for [f, D*, D].
8181
self.bounds = np.array([(0, 1), (5, 100), (0, 4)])
8282
elif (bounds[0][1] <= 1) or rescale_units: # Realistically, if mm2/s units are used, D* bound is <= 1

‎src/original/IAR_LundUniversity/ivim_fit_method_segmented_2step.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -86,13 +86,13 @@ def ivim_signal(self, b, S0, f, D_star, D):
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8787
def set_bounds(self, bounds):
8888
# Use this function for fits that uses curve_fit
89-
if bounds == None:
89+
if bounds is None:
9090
self.bounds = np.array([(0, 0, 0.005, 0), (np.inf, 1, 0.1, 0.004)])
9191
else:
92-
self.bounds = np.array([(0, *bounds[0]), (np.inf, *bounds[1])])
92+
self.bounds = np.array([bounds[0], bounds[1]])
9393

9494
def set_initial_guess(self, initial_guess):
95-
if initial_guess == None:
95+
if initial_guess is None:
9696
self.initial_guess = (1, 0.2, 0.03, 0.001)
9797
else:
9898
self.initial_guess = initial_guess

‎src/original/IAR_LundUniversity/ivim_fit_method_segmented_3step.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -105,13 +105,13 @@ def ivim_signal(self, b, S0, f, D_star, D):
105105

106106
def set_bounds(self, bounds):
107107
# Use this function for fits that uses curve_fit
108-
if bounds == None:
108+
if bounds is None:
109109
self.bounds = np.array([(0, 0, 0.005, 0), (np.inf, 1, 0.1, 0.004)])
110110
else:
111-
self.bounds = np.array([(0, *bounds[0]), (np.inf, *bounds[1])])
111+
self.bounds = np.array([bounds[0], bounds[1]])
112112

113113
def set_initial_guess(self, initial_guess):
114-
if initial_guess == None:
114+
if initial_guess is None:
115115
self.initial_guess = (1, 0.2, 0.03, 0.001)
116116
else:
117117
self.initial_guess = initial_guess

‎src/original/IAR_LundUniversity/ivim_fit_method_sivim.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -77,13 +77,13 @@ def sivim_model(self, b, S0, f, D):
7777

7878
def set_bounds(self, bounds):
7979
# Use this function for fits that uses curve_fit
80-
if bounds == None:
80+
if bounds is None:
8181
self.bounds = np.array([(0, 0, 0), (np.inf, 1, 0.004)])
8282
else:
83-
self.bounds = np.array([(0, *bounds[0]), (np.inf, *bounds[1])])
83+
self.bounds = np.array([bounds[0], bounds[1]])
8484

8585
def set_initial_guess(self, initial_guess):
86-
if initial_guess == None:
86+
if initial_guess is None:
8787
self.initial_guess = (1, 0.2, 0.001)
8888
else:
8989
self.initial_guess = initial_guess

‎src/original/IAR_LundUniversity/ivim_fit_method_subtracted.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -93,13 +93,13 @@ def perfusion_signal(self, b, S0, D_star):
9393

9494
def set_bounds(self, bounds):
9595
# Use this function for fits that uses curve_fit
96-
if bounds == None:
96+
if bounds is None:
9797
self.bounds = np.array([(0, 0, 0.005, 0), (np.inf, 1, 0.1, 0.004)])
9898
else:
99-
self.bounds = np.array([(0, *bounds[0]), (np.inf, *bounds[1])])
99+
self.bounds = np.array([bounds[0], bounds[1]])
100100

101101
def set_initial_guess(self, initial_guess):
102-
if initial_guess == None:
102+
if initial_guess is None:
103103
self.initial_guess = (1, 0.2, 0.03, 0.001)
104104
else:
105105
self.initial_guess = initial_guess

‎src/original/IAR_LundUniversity/simple_test_of_fits.py‎

Lines changed: 0 additions & 130 deletions
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