Merge pull request #12 from mjt320/develop

change AIF interpolation to linear
mjt320 · Feb 27, 2024 · f0ccec1 · f0ccec1
2 parents ca2f1fb + d4ff12e
commit f0ccec1
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Showing 17 changed files with 174 additions and 131 deletions.
diff --git a/.gitignore b/.gitignore
@@ -138,6 +138,7 @@ dmypy.json
 cython_debug/
 
 # User-specific stuff
+.idea/
 .idea/**/workspace.xml
 .idea/**/tasks.xml
 .idea/**/usage.statistics.xml

diff --git a/.idea/.gitignore b/.idea/.gitignore
diff --git a/.idea/.name b/.idea/.name
diff --git a/.idea/SEPAL.iml b/.idea/SEPAL.iml
diff --git a/.idea/codeStyles/Project.xml b/.idea/codeStyles/Project.xml
diff --git a/.idea/codeStyles/codeStyleConfig.xml b/.idea/codeStyles/codeStyleConfig.xml
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/.idea/modules.xml b/.idea/modules.xml
diff --git a/.idea/other.xml b/.idea/other.xml
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
diff --git a/demo/demo_fit_dce.ipynb b/demo/demo_fit_dce.ipynb
diff --git a/demo/demo_interpolation.ipynb b/demo/demo_interpolation.ipynb
diff --git a/demo/demo_pk_models.ipynb b/demo/demo_pk_models.ipynb
diff --git a/demo/demo_simulation.ipynb b/demo/demo_simulation.ipynb
diff --git a/pyproject.toml b/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "sepal"
-version = "1.0.1"
+version = "1.0.2"
 description = "Quantitative MRI processing"
 readme = "README.md"
 authors = [{ name = "Michael Thrippleton", email = "[email protected]" }]

diff --git a/src/sepal/aifs.py b/src/sepal/aifs.py
@@ -17,7 +17,6 @@
 from abc import ABC, abstractmethod
 
 import numpy as np
-from scipy.interpolate import interp1d, Akima1DInterpolator
 
 
 class AIF(ABC):
@@ -71,19 +70,11 @@ def __init__(self, t_data, c_ap_data):
         """
         self.t_data = t_data
         self.c_ap_data = c_ap_data
-        self.c_ap_func = Akima1DInterpolator(t_data, c_ap_data)
 
     def c_ap(self, t):
         """Get AIF plasma concentration(t). Overrides superclass method."""
         #  calculate concentration(t) using interpolation function
-        c_ap = self.c_ap_func(t)
-        #  replace values outside time range with first/last values
-        idx_before = t < min(self.t_data)
-        idx_after = t > max(self.t_data)
-        c_ap_before = self.c_ap_data[0]
-        c_ap_after = self.c_ap_data[-1]
-        c_ap[idx_before] = c_ap_before
-        c_ap[idx_after] = c_ap_after
+        c_ap = np.interp(t, self.t_data, self.c_ap_data)
         return c_ap