Fix return types

OSIPI · Jun 24, 2024 · cc13d2d · cc13d2d
1 parent c7aab27
commit cc13d2d
Showing 1 changed file with 45 additions and 49 deletions.
diff --git a/src/osipi/_signal_to_concentration.py b/src/osipi/_signal_to_concentration.py
@@ -10,36 +10,34 @@ def S_to_C_via_R1_SPGR(
     a: np.float64,
     r1: np.float64,
 ) -> NDArray[np.float64]:
-    """Signal to concentration via electromagnetic property
-        (SPGR, FXL, analytical, linear R1 relaxivity)
+    """
+    Signal to concentration via electromagnetic property (SPGR, FXL, analytical, linear R1 relaxivity)
 
     Converts S -> R1 -> C
 
     Args:
-        S (1D array of np.float64): vector of magnitude signals in a.u. [OSIPI code Q.MS1.001]
-        S_baseline (np.float64): pre-contrast magnitude signal in a.u. [OSIPI code Q.MS1.001]
-        R10 (np.float64): native longitudinal relaxation rate in units of /s. [OSIPI code Q.EL1.002]
-        TR (np.float64): repetition time in units of s. [OSIPI code Q.MS1.006]
-        a (np.float64): prescribed flip angle in units of deg. [OSIPI code Q.MS1.007]
-        r1 (np.float64): longitudinal relaxivity in units of /s/mM. [OSIPI code Q.EL1.015]
+        S (1D array of np.float64): Vector of magnitude signals in a.u. [OSIPI code Q.MS1.001]
+        S_baseline (np.float64): Pre-contrast magnitude signal in a.u. [OSIPI code Q.MS1.001]
+        R10 (np.float64): Native longitudinal relaxation rate in units of /s. [OSIPI code Q.EL1.002]
+        TR (np.float64): Repetition time in units of s. [OSIPI code Q.MS1.006]
+        a (np.float64): Prescribed flip angle in units of deg. [OSIPI code Q.MS1.007]
+        r1 (np.float64): Longitudinal relaxivity in units of /s/mM. [OSIPI code Q.EL1.015]
 
     Returns:
-        1D array of np.float64: vector of indicator total (across all compartments)
-            indicator concentration in units of mM. [OSIPI code Q.IC1.001]
+         NDArray[np.float64]: Vector of indicator total (across all compartments) indicator concentration in units of mM. [OSIPI code Q.IC1.001]
 
-    References/notes:
-        - Lexicon url: https://osipi.github.io/OSIPI_CAPLEX/perfusionProcesses/#
+    References:
+        - Lexicon URL: https://osipi.github.io/OSIPI_CAPLEX/perfusionProcesses/
         - Lexicon code: P.SC2.002
         - OSIPI name: ConvertSToCViaEP
         - Signal to electromagnetic property conversion method:
-            - model-based [OSIPI code P.SE1.001]
-                - Inversion method: analytical inversion [OSIPI code G.MI1.001]
-                - Forward model: Spoiled gradient recalled echo model [OSIPI code M.SM2.002]
+          - model-based [OSIPI code P.SE1.001]
+            - Inversion method: analytical inversion [OSIPI code G.MI1.001]
+            - Forward model: Spoiled gradient recalled echo model [OSIPI code M.SM2.002]
         - Electromagnetic property inverse model:
-            - model-based [OSIPI code P.EC1.001]
-                - Inversion method: analytical inversion [OSIPI code G.MI1.001]
-                - Forward model: longitudinal relaxation rate, linear with
-                - relaxivity model [OSIPI code M.EL1.003]
+          - model-based [OSIPI code P.EC1.001]
+            - Inversion method: analytical inversion [OSIPI code G.MI1.001]
+            - Forward model: longitudinal relaxation rate, linear with relaxivity model [OSIPI code M.EL1.003]
     """
     R1 = S_to_R1_SPGR(S, S_baseline, R10, TR, a)  # S -> R1
     return R1_to_C_linear_relaxivity(R1, R10, r1)  # R1 -> C
@@ -52,70 +50,68 @@ def S_to_R1_SPGR(
     TR: np.float64,
     a: np.float64,
 ) -> NDArray[np.float64]:
-    """Signal to electromagnetic property conversion (analytical, SPGR, FXL)
+    """
+    Signal to electromagnetic property conversion (analytical, SPGR, FXL)
 
     Converts Signal to R1
 
     Args:
-        S (1D array of np.float64): vector of magnitude signals in a.u. [OSIPI code Q.MS1.001]
-        S_baseline (np.float64): pre-contrast magnitude signal in a.u. [OSIPI code Q.MS1.001]
-        R10 (np.float64): native longitudinal relaxation rate in units of /S. [OSIPI code Q.EL1.002]
-        TR (np.float64): repetition time in units of s. [OSIPI code Q.MS1.006]
-        a (np.float64): prescribed flip angle in units of deg. [OSIPI code Q.MS1.007]
+        S (1D array of np.float64): Vector of magnitude signals in a.u. [OSIPI code Q.MS1.001]
+        S_baseline (np.float64): Pre-contrast magnitude signal in a.u. [OSIPI code Q.MS1.001]
+        R10 (np.float64): Native longitudinal relaxation rate in units of /s. [OSIPI code Q.EL1.002]
+        TR (np.float64): Repetition time in units of s. [OSIPI code Q.MS1.006]
+        a (np.float64): Prescribed flip angle in units of deg. [OSIPI code Q.MS1.007]
 
     Returns:
-        1D array of np.float64: vector of R1 in units of /s. [OSIPI code Q.EL1.001]
+        NDArray[np.float64]: Vector of R1 in units of /s. [OSIPI code Q.EL1.001]
 
-    References/notes:
-        - Lexicon url:
-        https://osipi.github.io/OSIPI_CAPLEX/perfusionProcesses/#https://osipi.github.io/OSIPI_CAPLEX/perfusionProcesses/#
+    References:
+        - Lexicon URL: https://osipi.github.io/OSIPI_CAPLEX/perfusionProcesses/#
         - Lexicon code: P.SE1.001
         - OSIPI name: model-based
-            - Inversion method: analytical inversion [OSIPI code G.MI1.001]
-            - Forward model: Spoiled gradient recalled echo model [OSIPI code M.SM2.002]
+          - Inversion method: analytical inversion [OSIPI code G.MI1.001]
+          - Forward model: Spoiled gradient recalled echo model [OSIPI code M.SM2.002]
         - Adapted from contribution of LEK_UoEdinburgh_UK
     """
-    # check S is a 1D array of floats
+    # Check S is a 1D array of floats
     if not (isinstance(S, np.ndarray) and S.ndim == 1 and S.dtype == np.float64):
         raise TypeError("S must be a 1D NumPy array of np.float64")
 
     a_rad = a * np.pi / 180
-    # estimate fully T1-relaxed signal S0 in units of a.u. [OSIPI code Q.MS1.010], then R1
+    # Estimate fully T1-relaxed signal S0 in units of a.u. [OSIPI code Q.MS1.010], then R1
     exp_TR_R10 = np.exp(-TR * R10)
     sin_a = np.sin(a_rad)
     cos_a = np.cos(a_rad)
     S0 = S_baseline * (1 - cos_a * exp_TR_R10) / (sin_a * (1 - exp_TR_R10))
     return np.log(((S0 * sin_a) - S) / (S0 * sin_a - (S * cos_a))) * (-1 / TR)  # R1
 
 
-def R1_to_C_linear_relaxivity(R1: NDArray[np.float64], R10: np.float64, r1: np.float64):
-    """Electromagnetic property inverse model:
-        longitudinal relaxation rate, linear with relaxivity
+def R1_to_C_linear_relaxivity(
+    R1: NDArray[np.float64], R10: np.float64, r1: np.float64
+) -> NDArray[np.float64]:
+    """
+    Electromagnetic property inverse model:
+    - longitudinal relaxation rate, linear with relaxivity
 
     Converts R1 to tissue concentration
 
     Args:
-        R1 (1D array of np.float64): vector of longitudinal
-            relaxation rate in units of /s. [OSIPI code Q.EL1.001]
-        R10 (np.float64): native longitudinal
-            relaxation rate in units of /s. [OSIPI code Q.EL1.002]
-        r1 (np.float64): longitudinal
-            relaxivity in units of /s/mM. [OSIPI code Q.EL1.015]
+        R1 (1D array of np.float64): Vector of longitudinal relaxation rate in units of /s. [OSIPI code Q.EL1.001]
+        R10 (np.float64): Native longitudinal relaxation rate in units of /s. [OSIPI code Q.EL1.002]
+        r1 (np.float64): Longitudinal relaxivity in units of /s/mM. [OSIPI code Q.EL1.015]
 
     Returns:
-        1D array of np.float64: vector of
-            indicator concentration in units of mM. [OSIPI code Q.IC1.001]
+        NDArray[np.float64]: Vector of indicator concentration in units of mM. [OSIPI code Q.IC1.001]
 
     References:
-        - Lexicon url: https://osipi.github.io/OSIPI_CAPLEX/perfusionProcesses/#
+        - Lexicon URL: https://osipi.github.io/OSIPI_CAPLEX/perfusionProcesses/#
         - Lexicon code: P.EC1.001
         - OSIPI name: model-based
-        - Inversion method: analytical inversion [OSIPI code G.MI1.001]
-        - Forward model: longitudinal relaxation rate,
-            linear with relaxivity model [OSIPI code M.EL1.003]
+          - Inversion method: analytical inversion [OSIPI code G.MI1.001]
+          - Forward model: longitudinal relaxation rate, linear with relaxivity model [OSIPI code M.EL1.003]
         - Adapted from equation given in lexicon
     """
-    # check R1 is a 1D array of floats
+    # Check R1 is a 1D array of floats
     if not (isinstance(R1, np.ndarray) and R1.ndim == 1 and R1.dtype == np.float64):
         raise TypeError("R1 must be a 1D NumPy array of np.float64")
     elif not (r1 >= 0):