Added the possibility of constraining with a fat fraction dataset

FatFractionLookup.py

@@ -76,7 +76,7 @@ class FatFractionLookup:
     NT2s = 60 # number of calculated T2 points
     NB1s = 20 # number of calculated B1 points
     MagPreparePulse = False
-    NFF = 100
+    NFF = 101
 
     def __init__(self, T2Limits, B1Limits, FatT2, NEchoes, EchoSpacing):
         self.fatT2 = FatT2
@@ -201,7 +201,7 @@ def getAllSignals(self):
                     curSignalIndex += 1
 
 
-        return parameterCombinations, signalsOut
+        return np.array(parameterCombinations), signalsOut
 
 
 

FatFractionLookup_GPU.py

@@ -21,14 +21,15 @@
 from __future__ import print_function
 
 import numpy as np
+import os.path
 
 from pycuda.autoinit import context
 import pycuda.gpuarray as ga
 from pycuda.compiler import SourceModule
 
 from FatFractionLookup import calcSliceprof, reduceSliceProf, FatFractionLookup
 
-CUDA_FILE = "epg.cu"
+CUDA_FILE = os.path.join( os.path.dirname(os.path.realpath(__file__)), "epg.cu")
 
 def getCudaFunction(nEchoes, echoSpacing, T1f, T1w, magPrep = False):
     # prepare definitions
@@ -59,7 +60,7 @@ class FatFractionLookup_GPU(FatFractionLookup):
     NT2s = 60 # number of calculated T2 points
     NB1s = 20 # number of calculated B1 points
     MagPreparePulse = False
-    NFF = 100
+    NFF = 101
 
     CudaBlockSize=256 # number of threads
 

dicomUtils.py

@@ -27,12 +27,10 @@ def load3dDicom(path):
     threeDData = None
     info = []
     l = os.listdir(basepath)
-    bar = Bar('Loading Dicom', max=100)
-    maxVal = len(l)
-    lastPercent = 0
-    currentFile = 0
+    bar = Bar('Loading Dicom', max=len(l))
     threeDlist = []
     for f in sorted(l):
+        if os.path.basename(f).startswith('.'): continue
         fname, ext = os.path.splitext(f)
         if ext.lower() in allowed_ext:
             try:
@@ -43,10 +41,7 @@ def load3dDicom(path):
                 info.append(dFile)
             except:
                 pass
-        currentFile += 1
-        if currentFile*100/maxVal > lastPercent:
-            bar.next()
-            lastPercent = currentFile*100/maxVal
+        bar.next()
     bar.finish()
     threeDData = np.stack(threeDlist, axis = 2)
 
@@ -82,10 +77,7 @@ def save3dDicom(volume, info, path, newSeriesNumber = None, newSeriesDescription
         fName = os.path.join(path, "image0001.dcm") # if one wants to save a part of a dataset
         dicom.write_file(fName, dicomFileData)
     else:
-        bar = Bar('Saving Dicom', max=100)
-        maxVal = len(info)
-        lastPercent = 0
-        currentFile = 0
+        bar = Bar('Saving Dicom', max=len(info))
         for sl in range(len(info)):
             dataArray = volume[...,sl]
             dicomFileData = copy.deepcopy(info[sl]) # create a copy of object
@@ -101,9 +93,5 @@ def save3dDicom(volume, info, path, newSeriesNumber = None, newSeriesDescription
 
             fName = os.path.join(path, "image%04d.dcm" % (sl+startImageNumber)) # if one wants to save a part of a dataset
             dicom.write_file(fName, dicomFileData)
-            currentFile += 1
-            if currentFile*100 / maxVal > lastPercent:
-                bar.next()
-                lastPercent = currentFile*100 / maxVal 
-        bar.finish()
-
+            bar.next()
+        bar.finish()

epg.cu

@@ -194,7 +194,7 @@ extern "C" void __global__ cpmg_sliceprof_B1_FF(unsigned int totalParameters, un
 {
     // calculate the cpmg signals for many values of B1 and Fat fractions
     const int index = blockIdx.x*blockDim.x + threadIdx.x;
-    if (index > totalParameters) return;
+    if (index >= totalParameters) return;
     float wT2 = parameters[index*3+0];
     float b1 = parameters[index*3+1];
     float ff = parameters[index*3+2];