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OSIPI · Jun 4, 2024 · 29a406a · 29a406a
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,10 +10,10 @@ repos:
 #    rev: 6.0.0
 #    hooks:
 #      - id: flake8
-#        args: [ '--max-line-length=80' ]
+#        args: [ '--max-line-length=70' ]
 
   - repo: https://github.com/psf/black
     rev: 23.3.0
     hooks:
       - id: black
-        args: [--line-length=80]
+        args: [--line-length=70]
diff --git a/docs/examples/tissue/plot_extended_tofts.py b/docs/examples/tissue/plot_extended_tofts.py
@@ -41,9 +41,13 @@
 
 # %%
 # Comparing different discretization methods for an extracellular volume fraction of 0.2, Ktrans of 0.2 /min and vp of 0.05
-ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0])  # Defaults to Convolution
+ct = osipi.extended_tofts(
+    t, ca, Ktrans, ve, vp[0]
+)  # Defaults to Convolution
 plt.plot(t, ct, "b-", label="Convolution")
-ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0], discretization_method="exp")
+ct = osipi.extended_tofts(
+    t, ca, Ktrans, ve, vp[0], discretization_method="exp"
+)
 plt.plot(t, ct, "g-", label="Exponential Convolution")
 plt.title(f"Ktrans = {Ktrans} /min")
 plt.xlabel("Time (sec)")

diff --git a/docs/examples/tissue/plot_tofts.py b/docs/examples/tissue/plot_tofts.py
@@ -40,9 +40,13 @@
 
 # %%
 # Comparing different discretization methods for an extracellular volume fraction of 0.2 and Ktrans of 0.2 /min
-ct = osipi.tofts(t, ca, Ktrans=Ktrans[1], ve=ve)  # Defaults to Convolution
+ct = osipi.tofts(
+    t, ca, Ktrans=Ktrans[1], ve=ve
+)  # Defaults to Convolution
 plt.plot(t, ct, "b-", label="Convolution")
-ct = osipi.tofts(t, ca, Ktrans=Ktrans[1], ve=ve, discretization_method="exp")
+ct = osipi.tofts(
+    t, ca, Ktrans=Ktrans[1], ve=ve, discretization_method="exp"
+)
 plt.plot(t, ct, "g-", label="Exponential Convolution")
 plt.title(f"Ktrans = {Ktrans[1]} /min")
 plt.xlabel("Time (sec)")

diff --git a/docs/source/generated/examples/tissue/plot_extended_tofts.py b/docs/source/generated/examples/tissue/plot_extended_tofts.py
@@ -41,9 +41,13 @@
 
 # %%
 # Comparing different discretization methods for an extracellular volume fraction of 0.2, Ktrans of 0.2 /min and vp of 0.05
-ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0])  # Defaults to Convolution
+ct = osipi.extended_tofts(
+    t, ca, Ktrans, ve, vp[0]
+)  # Defaults to Convolution
 plt.plot(t, ct, "b-", label="Convolution")
-ct = osipi.extended_tofts(t, ca, Ktrans, ve, vp[0], discretization_method="exp")
+ct = osipi.extended_tofts(
+    t, ca, Ktrans, ve, vp[0], discretization_method="exp"
+)
 plt.plot(t, ct, "g-", label="Exponential Convolution")
 plt.title(f"Ktrans = {Ktrans} /min")
 plt.xlabel("Time (sec)")

diff --git a/docs/source/generated/examples/tissue/plot_tofts.py b/docs/source/generated/examples/tissue/plot_tofts.py
@@ -40,9 +40,13 @@
 
 # %%
 # Comparing different discretization methods for an extracellular volume fraction of 0.2 and Ktrans of 0.2 /min
-ct = osipi.tofts(t, ca, Ktrans=Ktrans[1], ve=ve)  # Defaults to Convolution
+ct = osipi.tofts(
+    t, ca, Ktrans=Ktrans[1], ve=ve
+)  # Defaults to Convolution
 plt.plot(t, ct, "b-", label="Convolution")
-ct = osipi.tofts(t, ca, Ktrans=Ktrans[1], ve=ve, discretization_method="exp")
+ct = osipi.tofts(
+    t, ca, Ktrans=Ktrans[1], ve=ve, discretization_method="exp"
+)
 plt.plot(t, ct, "g-", label="Exponential Convolution")
 plt.title(f"Ktrans = {Ktrans[1]} /min")
 plt.xlabel("Time (sec)")

diff --git a/manage.py b/manage.py
@@ -67,7 +67,9 @@ def install():
     """Install requirements to a virtual environment"""
 
     logging.info("Installing requirements...")
-    os.system(activate() + " && " + "py -m pip install -r requirements.txt")
+    os.system(
+        activate() + " && " + "py -m pip install -r requirements.txt"
+    )
 
 
 if __name__ == "__main__":

diff --git a/src/osipi/_aif.py b/src/osipi/_aif.py
@@ -1,7 +1,9 @@
 import numpy as np
 
 
-def aif_parker(t: np.ndarray, BAT: float = 0.0, Hct: float = 0.0) -> np.ndarray:
+def aif_parker(
+    t: np.ndarray, BAT: float = 0.0, Hct: float = 0.0
+) -> np.ndarray:
     """AIF model as defined by Parker et al (2005)
 
     Args:
@@ -56,7 +58,10 @@ def aif_parker(t: np.ndarray, BAT: float = 0.0, Hct: float = 0.0) -> np.ndarray:
     # A2/(SD2*sqrt(2*PI)) * exp(-(t_offset-m2)^2/(2*var2))
     # A2 = 0.336, SD2 = 0.134, m2 = 0.364
     gaussian2 = 0.997356 * np.exp(
-        -1.0 * (t_offset - 0.365) * (t_offset - 0.365) / (2.0 * 0.132 * 0.132)
+        -1.0
+        * (t_offset - 0.365)
+        * (t_offset - 0.365)
+        / (2.0 * 0.132 * 0.132)
     )
     # alpha*exp(-beta*t_offset) / (1+exp(-s(t_offset-tau)))
     # alpha = 1.064, beta = 0.166, s = 37.772, tau = 0.482
@@ -113,7 +118,10 @@ def aif_georgiou(t: np.ndarray, BAT: float = 0.0) -> np.ndarray:
     """
 
     msg = "This function is not yet implemented \n"
-    msg += "If you implement it yourself, please consider submitting it as an OSIPI code contribution"
+    msg += (
+        "If you implement it yourself, please consider submitting it"
+        " as an OSIPI code contribution"
+    )
     raise NotImplementedError(msg)
 
 
@@ -156,5 +164,8 @@ def aif_weinmann(t: np.ndarray, BAT: float = 0.0) -> np.ndarray:
         >>> plt.plot(t,ca)
     """
     msg = "This function is not yet implemented \n"
-    msg += "If you implement it yourself, please consider submitting it as an OSIPI code contribution"
+    msg += (
+        "If you implement it yourself, please consider submitting it"
+        " as an OSIPI code contribution"
+    )
     raise NotImplementedError(msg)
diff --git a/src/osipi/_tissue.py b/src/osipi/_tissue.py
@@ -66,7 +66,10 @@ def tofts(
     """
     if not np.allclose(np.diff(t), np.diff(t)[0]):
         warnings.warn(
-            "Non-uniform time spacing detected. Time array may be resampled.",
+            (
+                "Non-uniform time spacing detected. Time array may be"
+                " resampled."
+            ),
             stacklevel=2,
         )
 
@@ -77,7 +80,9 @@ def tofts(
         # Convert units
         Ktrans = Ktrans / 60  # from 1/min to 1/sec
 
-        if discretization_method == "exp":  # Use exponential convolution
+        if (
+            discretization_method == "exp"
+        ):  # Use exponential convolution
             # Shift the AIF by the arterial delay time (if not zero)
             if Ta != 0:
                 f = interp1d(
@@ -118,7 +123,9 @@ def tofts(
             else:
                 # Resample at the smallest spacing
                 dt = np.min(np.diff(t))
-                t_resampled = np.linspace(t[0], t[-1], int((t[-1] - t[0]) / dt))
+                t_resampled = np.linspace(
+                    t[0], t[-1], int((t[-1] - t[0]) / dt)
+                )
                 ca_func = interp1d(
                     t,
                     ca,
@@ -219,7 +226,10 @@ def extended_tofts(
 
     if not np.allclose(np.diff(t), np.diff(t)[0]):
         warnings.warn(
-            "Non-uniform time spacing detected. Time array may be resampled.",
+            (
+                "Non-uniform time spacing detected. Time array may be"
+                " resampled."
+            ),
             stacklevel=2,
         )
 
@@ -230,7 +240,9 @@ def extended_tofts(
         # Convert units
         Ktrans = Ktrans / 60  # from 1/min to 1/sec
 
-        if discretization_method == "exp":  # Use exponential convolution
+        if (
+            discretization_method == "exp"
+        ):  # Use exponential convolution
             # Shift the AIF by the arterial delay time (if not zero)
             if Ta != 0:
                 f = interp1d(
@@ -272,7 +284,9 @@ def extended_tofts(
             else:
                 # Resample at the smallest spacing
                 dt = np.min(np.diff(t))
-                t_resampled = np.linspace(t[0], t[-1], int((t[-1] - t[0]) / dt))
+                t_resampled = np.linspace(
+                    t[0], t[-1], int((t[-1] - t[0]) / dt)
+                )
                 ca_func = interp1d(
                     t,
                     ca,
@@ -293,9 +307,9 @@ def extended_tofts(
                 convolution = np.convolve(ca_resampled, imp_resampled)
 
                 # Discard unwanted points, make sure time spacing is correct and add vp*ca term for extended model
-                ct_resampled = convolution[0 : len(t_resampled)] * t_resampled[
-                    1
-                ] + (vp * ca_resampled)
+                ct_resampled = convolution[
+                    0 : len(t_resampled)
+                ] * t_resampled[1] + (vp * ca_resampled)
 
                 # Restore time grid spacing
                 ct_func = interp1d(

diff --git a/tests/test_tissue.py b/tests/test_tissue.py
@@ -34,14 +34,18 @@ def test_tissue_tofts():
     t = np.arange(0, 6 * 60, 0.01)
     ca = osipi.aif_parker(t)
     ct_conv = osipi.tofts(t, ca, Ktrans=0.6, ve=0.2)
-    ct_exp = osipi.tofts(t, ca, Ktrans=0.6, ve=0.2, discretization_method="exp")
+    ct_exp = osipi.tofts(
+        t, ca, Ktrans=0.6, ve=0.2, discretization_method="exp"
+    )
     assert np.allclose(ct_conv, ct_exp, rtol=1e-4, atol=1e-3)
 
     # 5. Test that the ratio of the area under the ct and ca curves is approximately the extracellular volume
     t = np.arange(0, 6 * 60, 1)
     ca = osipi.aif_parker(t)
     ct_conv = osipi.tofts(t, ca, Ktrans=0.6, ve=0.2)
-    ct_exp = osipi.tofts(t, ca, Ktrans=0.6, ve=0.2, discretization_method="exp")
+    ct_exp = osipi.tofts(
+        t, ca, Ktrans=0.6, ve=0.2, discretization_method="exp"
+    )
     assert math.isclose(
         np.trapz(ct_conv, t) / np.trapz(ca, t), 0.2, abs_tol=1e-1
     )
@@ -55,13 +59,17 @@ def test_tissue_tofts():
     ct_conv = osipi.tofts(t, ca, Ktrans=0, ve=0.2)
     assert np.count_nonzero(ct_conv) == 0
 
-    ct_exp = osipi.tofts(t, ca, Ktrans=0, ve=0.2, discretization_method="exp")
+    ct_exp = osipi.tofts(
+        t, ca, Ktrans=0, ve=0.2, discretization_method="exp"
+    )
     assert np.count_nonzero(ct_exp) == 0
 
     ct_conv = osipi.tofts(t, ca, Ktrans=0.6, ve=0)
     assert np.count_nonzero(ct_conv) == 0
 
-    ct_exp = osipi.tofts(t, ca, Ktrans=0.6, ve=0, discretization_method="exp")
+    ct_exp = osipi.tofts(
+        t, ca, Ktrans=0.6, ve=0, discretization_method="exp"
+    )
     assert np.count_nonzero(ct_exp) == 0
 
 
@@ -81,7 +89,9 @@ def test_tissue_extended_tofts():
     # 3. The offset option - test that the tissue concentration is shifted from the AIF by the specified offset time
     t = np.arange(0, 6 * 60, 1)
     ca = osipi.aif_parker(t)
-    ct = osipi.extended_tofts(t, ca, Ktrans=0.6, ve=0.2, vp=0.3, Ta=60.0)
+    ct = osipi.extended_tofts(
+        t, ca, Ktrans=0.6, ve=0.2, vp=0.3, Ta=60.0
+    )
     assert (
         np.min(np.where(ct > 0.0)) - np.min(np.where(ca > 0.0)) - 1
     ) * 1 == 60.0