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Added estimation of phantom background via line definition in configuration #5

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1f73ec5
Added estimation of phantom background via line definition in configu…
MaxTousss Apr 14, 2024
5e86770
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MaxTousss Oct 15, 2025
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83 changes: 69 additions & 14 deletions computeDerenzoValleyToPeak.py
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Original file line number Diff line number Diff line change
Expand Up @@ -148,7 +148,7 @@ def loadImages(_imPath, _zIndex, _binFormat, _nImSpacing):
else:
listIm = [np.load(_imPath[i]).T for i in range(len(_imPath))]
else:
# We assume it is a series of images in dicom format
# We assume it is a series of images in dicom format
listIm, imSpacing = loadDicom_2DImages(_imPath)
elif len([cP for cP in _imPath if os.path.exists(cP)]) != len(_imPath):
tmp = [cP for cP in _imPath if not os.path.exists(cP)]
Expand Down Expand Up @@ -472,7 +472,7 @@ def genAllLpExtremumPos(_lpConfig):


def extractAllLineProfile(_im, _lpExtPos, _spotsSize, _imSpacing, _roiRatio, \
_lpSampleRate=10000):
_backgroundRoi=None, _lpSampleRate=10000):
"""
Def.: Extract the lines profile defined in _lpExtPos from _im. The lines profile are
segmented in a dictionnary of [sector, angle, row]. Each line profile is
Expand All @@ -485,6 +485,8 @@ def extractAllLineProfile(_im, _lpExtPos, _spotsSize, _imSpacing, _roiRatio, \
pixels.
@_roiRatio (Tuple, 2 Float): Ratio of the region of interest to keep. The first is
for the two spots and the second is for the background/valley.
@_backgroundRoi (List, 2 List, 2 floats): Starting and ending position of the line
used to compute the phantom background.
@_lpSampleRate (Integer): The number of samples used for the extraction of the
profiles from the image.
Return:
Expand All @@ -493,6 +495,23 @@ def extractAllLineProfile(_im, _lpExtPos, _spotsSize, _imSpacing, _roiRatio, \
"""
imSize = np.asarray(_im.shape) * _imSpacing

if _backgroundRoi is not None:
# Discretize line profile sampling.
x = np.linspace(_backgroundRoi[0][0], _backgroundRoi[1][0], _lpSampleRate)
y = np.linspace(_backgroundRoi[0][1], _backgroundRoi[1][1], _lpSampleRate)
# Extract the values of the line profile using nearest interpolation.
# TODO: Offer fancier interpolation?
# TODO: Make sure that x, y axis are always stored as _im[y, x]
x_indexSpace = np.floor(((x + (imSize[1] / 2.0)) / imSize[1]) * _im.shape[1])
x_indexSpace = x_indexSpace.astype(np.int32)
y_indexSpace = np.floor(((y + (imSize[0] / 2.0)) / imSize[0]) * _im.shape[0])
y_indexSpace = y_indexSpace.astype(np.int32)
# TODO: read and adapt orientation.
lineProfile = _im[:, :][y_indexSpace, x_indexSpace]
im = _im - np.mean(lineProfile)
else:
im = _im

# Init first level of the dictionnary
segLp = len(_lpExtPos) * [None,]
for cSect in range(len(_lpExtPos)):
Expand All @@ -507,9 +526,10 @@ def extractAllLineProfile(_im, _lpExtPos, _spotsSize, _imSpacing, _roiRatio, \
segLp[cSect][cAng][cRow] = len(_lpExtPos[cSect][cAng][cRow]) * [None,]
for cLp in range(len(_lpExtPos[cSect][cAng][cRow])):
currLp = _lpExtPos[cSect][cAng][cRow][cLp]
segLp[cSect][cAng][cRow][cLp] = extractLineProfile(_im, currLp, \
segLp[cSect][cAng][cRow][cLp] = extractLineProfile(im, currLp, \
cSpotSize, imSize, _roiRatio, \
_lpSampleRate)

return segLp


Expand Down Expand Up @@ -721,8 +741,8 @@ def lineProfilMetric_parabola(lineProfil):
segVal[cSeg] = min(np.max(segQuadFit), \
np.max(lineProfil[cSeg]["imVal"]))

val = min(segVal["valley"] / (0.5 * segVal["firstSpot"] + 0.5 * segVal["secSpot"]), \
1.0)
val = min((segVal["valley"]) / (0.5 * segVal["firstSpot"] \
+ 0.5 * segVal["secSpot"]), 1.0)

return val

Expand All @@ -731,11 +751,12 @@ def lineProfilMetric_parabola(lineProfil):
#########################################################################################
# Line profile configurations:
#########################################################################################
def loadLineProfileConfig(_lpConfigPath):
def loadLineProfileConfig(_lpConfigPath, _backgroundCorr):
'''
Def: Load the congiguration parameters for the lines profile.
@_lpConfigPath (Str): Path of the json with the configuration parameters for the
analysis.
asd
Return:
Dict
spotsSize: The size of the spots to study.
Expand All @@ -759,6 +780,19 @@ def loadLineProfileConfig(_lpConfigPath):
if lpConfig["triangle"].shape[1:] != (3, 2):
sys.exit("The triangle coordinates should be defined as three positions in 2D.")

if _backgroundCorr == True:
lpConfig["backgroundRoi"] = np.asarray(lpConfig["backgroundRoi"])
if "backgroundRoi" not in lpConfig:
sys.exit("The background correction flag was raised but it is not defined " \
"in the configuration file.")
if lpConfig["backgroundRoi"].shape != (2, 2):
sys.exit("The definition of the background ROI is supposed to be two " \
"positions in 2D. This is not the case in the configuration " \
"provided.")
# asd plus de check?
else:
lpConfig["backgroundRoi"] = None

return lpConfig


Expand Down Expand Up @@ -1214,7 +1248,7 @@ def showSpotsPosOnImage(_im, _imSpacing, _lpConfig, _spotsCenter, _savePath):


def showLinesProfileOnImage(_im, _imSpacing, _lpConfig, _spotsCenter, _lpExtPos,
_savePath):
_savePath, _backgroundCorr):
"""
Def.: Show the lines profile defined in the configuration file superposed on _im.
@_im (2D numpy array): The image to study.
Expand All @@ -1225,6 +1259,8 @@ def showLinesProfileOnImage(_im, _imSpacing, _lpConfig, _spotsCenter, _lpExtPos,
@_lpExtPos (list of lists): Edges of every line profile arranged as
[nbSector, nbAngle, nbRow, nbLpCurrSectorAndRow, ptsExt, nDim]
@_savePath (Str): Path where to save the figure.
@_backgroundCorr (Boolean): If a line was defined in the configuration to estimate
the background, show where the line is on the image.
TODO: Possibly 1 on 1.5 pixels offset.
TODO: Add an option for seeing subset of line profile?
"""
Expand Down Expand Up @@ -1262,6 +1298,13 @@ def showLinesProfileOnImage(_im, _imSpacing, _lpConfig, _spotsCenter, _lpExtPos,
plt.fill(np.append(oneSide[:, 0], otherSide[::-1, 0]), \
np.append(oneSide[:, 1], otherSide[::-1, 1]), \
color=color[cAng])

if _backgroundCorr == True:
bckgLine = _lpConfig["backgroundRoi"]
plt.fill([bckgLine[0, 0], bckgLine[1, 0]], [bckgLine[0, 1], bckgLine[1, 1]], \
color='y')


plt.tight_layout(pad=0)
if _savePath is None:
plt.show()
Expand Down Expand Up @@ -1363,8 +1406,10 @@ def cropImage(_im, _imSpacing, _minIntensityFrac=0.02):
xOutside = lpConfig['triangle'][:, 1:, 0].flatten()
yOutside = lpConfig['triangle'][:, 1:, 1].flatten()
offsetSpotSize = int(np.max(lpConfig['spotsSize']) / _imSpacing[0])
xWidthInIdxs = int((xOutside.max() - xOutside.min()) / _imSpacing[0]) + offsetSpotSize
yWidthInIdxs = int((yOutside.max() - yOutside.min()) / _imSpacing[1]) + offsetSpotSize
xWidthInIdxs = int((xOutside.max() - xOutside.min()) / _imSpacing[0]) \
+ offsetSpotSize
yWidthInIdxs = int((yOutside.max() - yOutside.min()) / _imSpacing[1]) \
+ offsetSpotSize

if ((idxsEdges[1][1] - idxsEdges[1][0]) > xWidthInIdxs) and \
((idxsEdges[0][1] - idxsEdges[0][0]) > yWidthInIdxs):
Expand Down Expand Up @@ -1473,7 +1518,6 @@ def simplifyImagesName(_imName):
if tmp != "":
for i in range(len(_imName)):
_imName[i] = _imName[i][len(redondantPart):]

return _imName


Expand Down Expand Up @@ -1581,6 +1625,11 @@ def parserCreator():
parser.add_argument('--simplifyName', action='store_true', required=False, \
dest='simplifyName', default=False, \
help='When saving results, simplify the image name.')
parser.add_argument('--backgroundCorr', action='store_true', required=False,\
dest='backgroundCorr', default=False, \
help='Estimate the phantom background value using the line ' \
'defined in the configuration file.')

parser.add_argument('--configurationHelper', action='store_true',
help="Start the corner positionning tool, this updates the config"
" and prevents analysis from running")
Expand Down Expand Up @@ -1638,7 +1687,7 @@ def argsValidator(_args):
listIm, imSpacing = loadImages(args.imPath, args.zIndex, binFormat, \
args.nSpacing)

lpConfig = loadLineProfileConfig(args.lpConfigPath)
lpConfig = loadLineProfileConfig(args.lpConfigPath, args.backgroundCorr)

if args.configurationHelper:
runConfigurationHelper(listIm[args.imageShown], imSpacing, lpConfig, args.lpConfigPath)
Expand All @@ -1655,7 +1704,8 @@ def argsValidator(_args):
args.pathForFigures)
if args.showLinesProfile == True:
showLinesProfileOnImage(listIm[args.imageShown], imSpacing, lpConfig,
spotsCenter, lpExtPos, args.pathForFigures)
spotsCenter, lpExtPos, args.pathForFigures,
args.backgroundCorr)

if args.saveResults != None:
resultArray = -np.ones(shape=(len(listIm), 3 * len(lpConfig["spotsSize"])))
Expand All @@ -1667,7 +1717,7 @@ def argsValidator(_args):
args.stackofIt)

segLp = extractAllLineProfile(im, lpExtPos, lpConfig["spotsSize"], imSpacing, \
args.roiRatio)
args.roiRatio, lpConfig["backgroundRoi"])
results = computeSectorValleyToPeak(segLp, args.metric, args.roiRatio,
args.showVprHistos, imSpacing,
cFigSavePath)
Expand All @@ -1680,6 +1730,7 @@ def argsValidator(_args):
print(f"ROI on peaks : {100.0 * args.roiRatio[0]:.0f}%")
print(f"ROI on valleys : {100.0 * args.roiRatio[1]:.0f}%")
print('Rod size (mm) : ', end='')

for i,v in enumerate(results[0]):
if v < RAYLEIGH_CRITERION:
print(fmtResolved(lpConfig['spotsSize'][i], '.3f') + '\t', end='')
Expand All @@ -1705,7 +1756,11 @@ def argsValidator(_args):
resultArray[l, nbSpot:(2 * nbSpot)] = np.round(results[1], 3)
resultArray[l, (2 * nbSpot):] = results[2]
# Remove file extention from name
imName[l] = cImName.rsplit( ".", 1)[0]
if args.stackofIt == True:
imName[l] = cImName
else:
imName[l] = cImName.rsplit(".", 1)[0]


if args.saveResults != None:
iterables = [["Average VPR", "Stdev VPR", "Resolvability [%]"], \
Expand Down