Merge pull request #34 from OSIPI/dev

Functionality for one pipeline

docs/examples/signal/plot_signal_SPGR.py

@@ -0,0 +1,29 @@
+"""
+==============
+Linear model for relationship between R1 and magnitude signal
+==============
+
+Demonstrating the linear model for relationship between R1 and magnitude signal, s = k.R1
+"""
+
+# %%
+# Import necessary packages
+import matplotlib.pyplot as plt
+import numpy as np
+import osipi
+
+# %%
+# Convert a series of R1 values to the corresponding signal intensities using the SPGR model.
+
+R1 = np.linspace(0.1, 10, 50)  # R1 in units of /s.
+S0 = np.float64(100)  # fully T1-relaxed signal in a.u.
+TR = np.float64(5e-3)  # repetition time in units of s.
+a = np.float64(15)  # prescribed flip angle in units of deg.
+S = osipi.signal_SPGR(R1, S0, TR, a)  # signal in a.u.
+print(f"Signal: {S}")
+
+# Plot S vs. R1
+plt.plot(R1, S, "r-")
+plt.xlabel("R1 (/s)")
+plt.ylabel("S (a.u.)")
+plt.show()

docs/examples/signal/plot_signal_linear.py

@@ -0,0 +1,27 @@
+"""
+==============
+Linear model for relationship between R_1 and magnitude signal S
+==============
+
+Demonstrating the linear model for relationship between R_1 and magnitude signal, S = k.R_1
+"""
+
+# %%
+# Import necessary packages
+import matplotlib.pyplot as plt
+import numpy as np
+import osipi
+
+# %%
+# Convert a series of R1 values to the corresponding signal intensities.
+
+R1 = np.array([0.0, 1.5, 3.0, 4.0, 10.0])  # R_1 in units of /s
+k = np.float64(150.0)  # constant of proportionality in units of a.u. s
+S = osipi.signal_linear(R1, k)  # signal in a.u.
+print(f"Signal: {S}")
+
+# Plot S vs. R1
+plt.plot(R1, S, "ro-")
+plt.xlabel("R1 (/s)")
+plt.ylabel("S (a.u.)")
+plt.show()

docs/examples/signal_to_concentration/plot_signal_to_concentration_R1_to_C_linear_relaxivity.py

@@ -0,0 +1,29 @@
+"""
+==============
+Electromagnetic property inverse model: longitudinal relaxation rate, linear with relaxivity
+==============
+
+Demonstrating the inverse linear relaxivity model
+    for converting R_1 to tissue indicator concentration C.
+"""
+
+# %%
+# Import necessary packages
+import matplotlib.pyplot as plt
+import numpy as np
+import osipi
+
+# %%
+# Convert a series of R1 values to the corresponding indicator concentrations.
+R1 = np.array([1, 2, 3, 4, 5, 6], dtype=np.float64)
+R10 = np.float64(1)
+r1 = np.float64(5)
+
+C = osipi.R1_to_C_linear_relaxivity(R1, R10, r1)
+print(f"Concentration (mM): {C}")
+
+# Plot C vs. R1
+plt.plot(R1, C, "r-")
+plt.xlabel("R1 (/s)")
+plt.ylabel("C (mM)")
+plt.show()

docs/examples/signal_to_concentration/plot_signal_to_concentration_S_to_C_via_R1_SPGR.py

@@ -0,0 +1,69 @@
+"""
+==============
+Signal to concentration via electromagnetic property (SPGR, FXL, analytical linear relaxivity)
+==============
+
+Demonstrating the SPGR model for relationship between
+    signal S and total tissue indicator concentration, assuming the FXL.
+"""
+
+# %%
+# Import necessary packages
+import matplotlib.pyplot as plt
+import numpy as np
+import osipi
+
+# %%
+# Convert a series of S values to the corresponding indicator concentrations.
+# Example data adapted from OSIPI repository ("vox_1")
+S = np.array(
+    [
+        7,
+        9,
+        6,
+        10,
+        9,
+        6,
+        9,
+        10,
+        9,
+        9,
+        9,
+        12,
+        8,
+        10,
+        12,
+        15,
+        53,
+        70,
+        71,
+        70,
+        63,
+        58,
+        54,
+        50,
+        53,
+        48,
+        52,
+        49,
+        42,
+    ],
+    dtype=np.float64,
+)
+S_baseline = S[0]  # use first point for baseline signal
+R10 = np.float64(1 / 1.4)
+TR = np.float64(0.002)
+a = np.float64(13)
+r1 = np.float64(4.5)
+
+C = osipi.S_to_C_via_R1_SPGR(S, S_baseline, R10, TR, a, r1)
+print(f"Concentration (mM): {C}")
+
+# Plot S and C
+fig, ax = plt.subplots(2, 1)
+ax[0].plot(S, "b-")
+ax[0].set_ylabel("S (a.u.)")
+ax[1].plot(C, "b-")
+ax[1].set_ylabel("C (mM)")
+ax[1].set_xlabel("time point")
+plt.show()

docs/examples/signal_to_concentration/plot_signal_to_concentration_S_to_R1_SPGR.py

@@ -0,0 +1,67 @@
+"""
+==============
+Signal to electromagnetic properties (R1) (SPGR, FXL, analytical linear relaxivity)
+==============
+
+Demonstrating the SPGR model for relationship between signal S and R1, assuming the FXL.
+"""
+
+# %%
+# Import necessary packages
+import matplotlib.pyplot as plt
+import numpy as np
+import osipi
+
+# %%
+# Convert a series of S values to the corresponding R1 values.
+# Example data adapted from OSIPI repository ("vox_1")
+S = np.array(
+    [
+        7,
+        9,
+        6,
+        10,
+        9,
+        6,
+        9,
+        10,
+        9,
+        9,
+        9,
+        12,
+        8,
+        10,
+        12,
+        15,
+        53,
+        70,
+        71,
+        70,
+        63,
+        58,
+        54,
+        50,
+        53,
+        48,
+        52,
+        49,
+        42,
+    ],
+    dtype=np.float64,
+)
+S_baseline = np.float64(S[0])  # use first point for baseline signal
+R10 = np.float64(1 / 1.4)
+TR = np.float64(0.002)
+a = np.float64(13)
+
+R1 = osipi.S_to_R1_SPGR(S, S_baseline, R10, TR, a)
+print(f"R_1 (/s): {R1}")
+
+# Plot S and R1
+fig, ax = plt.subplots(2, 1)
+ax[0].plot(S, "b-")
+ax[0].set_ylabel("S (a.u.)")
+ax[1].plot(R1, "b-")
+ax[1].set_ylabel("R1 (/s)")
+ax[1].set_xlabel("time point")
+plt.show()

docs/source/reference/alphabetical.rst

@@ -10,8 +10,10 @@ Alphabetic list of all currently available `osipi` code snippets.
    :toctree: ../generated/api/
    :template: autosummary.rst
 
-   aif_parker
    aif_georgiou
+   aif_parker
    aif_weinmann
-   tofts
    extended_tofts
+   signal_linear
+   signal_SPGR
+   tofts

docs/source/reference/general.convolution.rst

@@ -3,10 +3,11 @@ Convolution
 
 .. currentmodule:: osipi
 
-.. note::
+Exponential convolution
+-----------------------
 
-    This is a placeholder page. There is no relevant functionality in ``osipi`` yet.
+.. autosummary::
+   :toctree: ../generated/api/
+   :template: autosummary.rst
 
-    Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to..
-
-    See :ref:`developer-guide` for guidance on how to contribute.
+   exp_conv

docs/source/reference/models.signal.rst

@@ -3,10 +3,13 @@ Signal models
 
 .. currentmodule:: osipi
 
-.. note::
 
-    This is a placeholder page. There is no relevant functionality in ``osipi`` yet.
+Magnitude models: DCE - R1 in the fast water exchange limit
+-----------------------------------------------------------
 
-    Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to..
+.. autosummary::
+   :toctree: ../generated/api/
+   :template: autosummary.rst
 
-    See :ref:`developer-guide` for guidance on how to contribute.
+   signal_linear
+   signal_SPGR

docs/source/reference/processes.R1.rst

@@ -3,10 +3,12 @@ R1 measurement
 
 .. currentmodule:: osipi
 
-.. note::
 
-    This is a placeholder page. There is no relevant functionality in ``osipi`` yet.
+Signal to R1
+---------------
 
-    Please check back later - or better yet, write up what you were looking for here and contribute it! This way the next person looking for this feature won't have to..
+.. autosummary::
+   :toctree: ../generated/api/
+   :template: autosummary.rst
 
-    See :ref:`developer-guide` for guidance on how to contribute.
+   S_to_R1_SPGR