Merge pull request #22 from OSIPI/main

merge main to brain_phantom

Author: oscarjalnefjord

doc/code_contributions_record.csv

@@ -15,4 +15,5 @@ IVIM,Fitting,Variable projection,See referenced article. Supports units in mm2/s
 IVIM,Fitting,Linear fit,Linear fit for D with extrapolation for f. Supports units in mm2/s and µm2/ms,IAR_LundUniversity,TF2.4_IVIM-MRI_CodeCollection/src/original/IAR_LundUniversity/ivim_fit_method_modified_linear.py,Modified by Ivan A. Rashid,Lund University,IvimModelLinear,tba,tbd,
 IVIM,Fitting,sIVIM fit,NLLS of the simplified IVIM model (sIVIM). Supports units in mm2/s and µm2/ms,IAR_LundUniversity,TF2.4_IVIM-MRI_CodeCollection/src/original/IAR_LundUniversity/ivim_fit_method_modified_sivim.py,Modified by Ivan A. Rashid,Lund University,IvimModelsIVIM,tba,tbd,
 IVIM,Fitting,Segmented NLLS fitting,MATLAB code,OJ_GU,TF2.4_IVIM-MRI_CodeCollection/src/original/OJ_GU/,Oscar Jalnefjord,University of Gothenburg,IVIM_seg,https://doi.org/10.1007/s10334-018-0697-5,tbd,
-IVIM,Fitting,Bayesian,MATLAB code,OJ_GU,TF2.4_IVIM-MRI_CodeCollection/src/original/OJ_GU/,Oscar Jalnefjord,University of Gothenburg,IVIM_bayes,https://doi.org/10.1002/mrm.26783,tbd,
+IVIM,Fitting,Bayesian,MATLAB code,OJ_GU,TF2.4_IVIM-MRI_CodeCollection/src/original/OJ_GU/,Oscar Jalnefjord,University of Gothenburg,IVIM_bayes,https://doi.org/10.1002/mrm.26783,tbd,
+IVIM,Fitting,Linear fit,Linear fit for D and D* and f. Intended to be extremely fast but not always accurate,ETP_SRI,TF2.4_IVIM-MRI_CodeCollection/src/original/ETP_SRI/LinearFitting.py,Eric Peterson,SRI International,,,tbd,

src/original/PvH_KB_NKI/DWI_Examples.py

@@ -0,0 +1,57 @@
+"""
+Created on Aug 30 2022
+
+Script to demonstrate usage of standalone DWI functions:
+Generate_ADC
+Generate_IVIMmaps
+
+@authors: s.zijlema, p.vhoudt, k.baas, e.kooreman
+Group: Uulke van der Heide - NKI 
+"""
+
+import numpy as np
+from DWI_functions_standalone import generate_ADC_standalone, generate_IVIMmaps_standalone
+import matplotlib.pyplot as plt
+import pathlib
+
+#Load some DWI data
+file=pathlib.Path(__file__)
+file_path = file.with_name('IVIM_b0_15_150_500.npy').as_posix()
+DWI_data = np.load(file_path)
+
+# Specify b values that are in the data
+bvalues = [0, 15, 150, 500]
+
+# Specifiy if you want to plot the results
+plot_results = False
+
+# Generate ADC map and define the min and max b value that will be used for ADC fitting
+ADClog, b0_intercept, used_bvalues = generate_ADC_standalone(DWI_data,bvalues, bmin=150, bmax=500)
+
+# Generate ADC and define the min and max b value that will be used for ADC fitting as well as the max b value
+# that will be used for separate Dstar fitting
+ADClog, perfFrac, Dstar = generate_IVIMmaps_standalone(DWI_data, bvalues, bminADC=150, bmaxADC=500, bmaxDstar=150)
+Slice = 5
+
+if plot_results == True:
+    # Plot the ADC, f and D* maps
+    fig, axes = plt.subplots(1, 3, figsize=(10, 5))
+
+    axes[0].imshow(ADClog[:,Slice,:], cmap='viridis', vmin=0, vmax=5)
+    axes[0].set_title("ADC")
+    axes[0].axis('off')
+
+    axes[1].imshow(perfFrac[:,Slice,:], cmap='viridis', vmin=0, vmax=1)
+    axes[1].set_title("f map")
+    axes[1].axis('off')
+
+    axes[2].imshow(Dstar[:,Slice,:], cmap='viridis', vmin=0, vmax=200)
+    axes[2].set_title("D*")
+    axes[2].axis('off')
+
+    plt.tight_layout()  # Adjust spacing between subplots
+    plt.show()
+
+print("finish")
+
+

src/original/PvH_KB_NKI/DWI_functions_standalone.py

@@ -0,0 +1,239 @@
+# -*- coding: utf-8 -*-
+"""
+DWI_functions.py
+====================================
+This module can be used to calculate ADC/IVIM maps.
+IVIM fitting is done in a segmented fashion: https://doi.org/10.3389/fonc.2021.705964
+
+@authors: s.zijlema, p.vhoudt, k.baas, e.kooreman
+Group: Uulke van der Heide - NKI
+"""
+
+import numpy as np
+
+def generate_ADC_standalone(DWIdata, bvalues, bmin: int = 150, bmax: int = 1000, specificBvals: list = []):
+    """
+    Function to create an ADC map from DWI data.
+    Required input is a numpy array with the data and the corresponding b-values
+
+    Example use:
+    generate_ADC(data, bvalues)
+
+    Parameters
+    ---------
+    DWIdata: numpy array
+        DWI data
+    bvalues: list
+        bvalues corresponding to the data
+    bmin/bmax (optional)
+        Used to select range of b-values that you want to include to calculate the ADC.
+        Not used when specificBvals is defined.
+    specificBvals (optional)
+        List of b-values that should be used for ADC map calculation.
+        If set, bmin/bmax options are not used.
+
+    Returns
+    -------
+    ADClog
+        ADC map
+    b0_intercept
+        Map with y-intercepts (b=0) of ADC fit
+    bvalues
+        b-values that matched the criteria
+    """
+
+    #Obtain indices of matching b-values
+    if specificBvals == []:
+        #Select only b-values >=bmin and <=bmax
+        bvalueindex = [i for i,v in enumerate(bvalues) if v >= bmin and v <= bmax]
+    else: #manual b-value selection
+        #Check if all specified b-values were acquired
+        if not all(elem in bvalues for elem in specificBvals):
+            raise Exception('Not all specified b-values were found. Available b-values: '+str(bvalues)+'. You requested: '+str(specificBvals))
+        #Get b-value indices
+        bvalueindex = [i for i,v in enumerate(bvalues) if v in specificBvals]
+
+    use_bvalues = [bvalues[index] for index in bvalueindex]
+    if len(use_bvalues) < 2:
+        raise Exception('Less than 2 b values were found that fulfill your min and max criteria.')
+
+    # Calculate ADC map using linear regression
+    ADClog, b0_intercept = fit_ADCmap_loglinear_standalone(DWIdata, bvalues, use_bvalues)
+    ADClog[ADClog<0] = 0 #set values below zero to zero
+
+    return ADClog, b0_intercept, use_bvalues
+
+def generate_IVIMmaps_standalone(DWIdata, bvalues, bminADC=150, bmaxADC=1000, bmaxDstar=50):
+    """
+    Function to calculate IVIM maps (perfusion fraction and D*).
+    NOTE: D* is calculated using only the lowest two b-values.
+
+    Example use:
+    generate_IVIMmaps(data, bvalues)
+
+    Parameters
+    ---------
+    DWIdata: numpy array
+        DWI data
+    bvalues: list
+        bvalues corresponding to the data
+    bminADC/bmaxADC (optional)
+        Used to select the range of b-values for ADC calculation.
+    bmaxDstar (optional)
+        Used to select the b-values for D* calculation.
+    outputOptions
+        ['ADC','f','D*'] (default) will output the ADC, f, and D*.
+
+
+    """
+
+    # Calculate ADC map
+    ADClog, b0_intercept, used_bvalues = generate_ADC_standalone(DWIdata, bvalues, bminADC, bmaxADC)
+
+    # Check if b=0 is acquired, otherwise f and D* cannot be calculated
+    if not 0 in bvalues:  # if b=0 is not acquired
+        print('B=0 is not available. Hence, only the ADC is calculated.')
+        return  # stop execution
+
+    # Get b0 data
+    b0index = bvalues.index(0)  # gets first index of b=0
+    DWIb0 = DWIdata[:, :, :, b0index]  # b=0 data
+
+    #### Calculate perfusion fraction
+    with np.errstate(divide='ignore', invalid='ignore'):  # hide division by 0 warnings
+        perfFrac = (DWIb0 - np.exp(b0_intercept)) / DWIb0  # perfusion fraction
+    perfFrac[np.isnan(perfFrac)] = 0
+    perfFrac[np.isinf(perfFrac)] = 0
+    perfFrac[perfFrac < 0] = 0  # f <0 is not possible
+    perfFrac[perfFrac > 1] = 1  # f >1 is also not possible
+
+    # Get matching b-values
+    try:
+        _, bvalues = select_b_values_standalone(bvalues, bmin=0, bmax=bmaxDstar)
+
+        # Check if b=0 was acquired
+        if 0 not in bvalues:
+            raise Exception('b=0 was not acquired')
+
+        if len(bvalues) > 2:
+            print('More than two b-values were detected for D* calculation. ' +
+                  'Note that only the first two will be used for D*.')
+
+    except Exception as e:
+        print("Could not calculate D* due to an error: " + str(e))
+        return
+
+    # Use b=0 and the lowest b-value to calculate D*
+    with np.errstate(divide='ignore', invalid='ignore'):  # hide division by 0 warnings
+        Dstar = -np.log(
+            (DWIdata[:,:,:,1] / DWIdata[:,:,:,0] - (1 - perfFrac) * np.exp(-bvalues[1] * 0.001 * ADClog)) / perfFrac) / \
+                bvalues[1]  # Calculate D* using f, d, and the lowest 2 b-values
+    Dstar[np.isnan(Dstar)] = 0
+    Dstar[np.isinf(Dstar)] = 0
+    Dstar = Dstar * 1000  # scale to same as ADC
+
+    return ADClog, perfFrac, Dstar
+
+
+def select_b_values_standalone(all_bvalues, bmin=0, bmax=float("inf"), specificBvals: list = []):
+    """
+    Find b-values and their indices between bmin and bmax of a scan (bmin <= b <= b max)
+    or of b-values that are defined in specificBvals.
+    If specificBvals is defined, only b-values are returned that are acquired
+    in the scan AND are present in specificBvals.
+
+    Parameters
+    ----------
+    all_bvalues : list of int
+        All b values that are in the data in the order that they are stored
+    bmin : int
+        Minimal b-value.
+    bmax : int
+        Maximal b-value.
+    specificBvals : list
+        List of b-values.
+
+
+    Returns
+    -------
+    bvalueindex : list of int
+        Indices of b-values between bmin and bmax.
+    bvalues : list of int
+        B-values between bmin and bmax.
+
+    """
+
+    # Obtain indices of matching b-values
+    if specificBvals == []:
+        # Select only b-values >=bmin and <=bmax
+        bvalueindex = [i for i, v in enumerate(all_bvalues) if v >= bmin and v <= bmax]
+    else:  # manual b-value selection
+        # Check if all specified b-values were acquired
+        if not all(elem in all_bvalues for elem in specificBvals):
+            raise Exception('Not all specified b-values were found. Available b-values: ' + str(
+                all_bvalues) + '. You requested: ' + str(specificBvals))
+
+        # Get b-value indices
+        bvalueindex = [i for i, v in enumerate(all_bvalues) if v in specificBvals]
+
+    # Check if enough b-values were found
+    if len(bvalueindex) < 2:
+        raise Exception("No(t enough) b-values matched the selected range between " + str(bmin) + " and " + str(
+            bmax) + " (found: " + str(len(bvalueindex)) + ")")
+
+    # Select matching b-values
+    bvalues = [all_bvalues[i] for i in bvalueindex]
+
+    # Return index and b-values
+    return bvalueindex, bvalues
+
+
+def fit_ADCmap_loglinear_standalone(DWIdata, all_bvalues, use_bvalues, size=[]):
+    """
+    Function to calculate ADC based on linear regression.
+    Taken from ADC_functions.py but adjusted to also output intercept and
+    removed size input requirement (could be extracted from si_array).
+    The ADC values have been validated with the Philips ADC maps (2022).
+
+    Parameters
+    ---------
+    DWIdata
+        DWI data
+    all_bvalues
+        list or array of b-values that are stored in the data
+    use_bvalues
+        list or array of selected b-values selected for calculation.
+
+    Returns
+    -------
+        ADC calculated ADC and the intercept with the y-axis at b=0 in the same
+        x,y,z coordinates as the original DWI image (i.e. size)
+
+    """
+
+    nr_bvalues = len(use_bvalues)
+
+    b_mat = np.ones([nr_bvalues, 2])
+    for curBvalNr in range(nr_bvalues):
+        b_mat[curBvalNr, 0] = use_bvalues[curBvalNr]
+
+    if size == []:
+        size = DWIdata.shape[:-1] # b-values are stored in the last dimension
+
+    # Extract the b values that are used for calculation
+    indices = [all_bvalues.index(value) for value in use_bvalues]
+    DWIdata = DWIdata[:,:,:,indices]
+    DWIdata = DWIdata.transpose(3, 0, 1, 2) # code below expects different format
+
+    with np.errstate(divide='ignore', invalid='ignore'):  # hide division by 0 warnings
+        log_si = -np.log(DWIdata.reshape(nr_bvalues, -1))  # calculate log of data and reshape to one row per b-value
+        #log_si = -np.log(DWIdata.reshape(-1, nr_bvalues))
+    log_si[np.isinf(log_si)] = 0  # to fix 0 values in si_array
+
+    ADC, intercept = np.linalg.lstsq(b_mat, log_si, rcond=None)[0]  # calculate ADC and b=0 intercept
+    ADC = ADC.reshape(*size) * 1000  # Convert ADC to 10^-3 mm^2/s
+    b0_intercept = -intercept.reshape(*size)  # can be used to calculate perfusion fraction
+
+    return ADC, b0_intercept
+
+