def test_coreFunction_small():
"""
Testing FarsighOPConv.app.coreFunction with a short runtime case
"""
testLabelFile = os.path.join(
"tests", "files", "Act5C_no5_med1_C428_dec1_label_20LabelSubset.tif")
testSeedsFile = os.path.join(
"tests", "files",
"Act5C_no5_med1_C428_dec1_seedPoints_20LabelSubset.txt")
expOutLabelFile = os.path.join(
"tests", "files",
"Act5C_no5_med1_C428_dec1_label_20LabelSubset_corrected32Bit_exp.tiff")
expOutXLFile = os.path.join(
"tests", "files",
"Act5C_no5_med1_C428_dec1_label_20LabelSubset_corrected32Bit_exp.xlsx")
print(f"Running tests using\n{testLabelFile} and\n{testSeedsFile}")
startTime = time.time()
outLabelFile, outXLFile = farsightOPConvAndMetrics(testLabelFile,
testSeedsFile)
endTime = time.time()
duration = endTime - startTime
print(f"Execution time of core Function: {duration/60}min")
assert np.allclose(tifffile.imread(outLabelFile),
tifffile.imread(expOutLabelFile))
assert pd.read_excel(outXLFile).equals(pd.read_excel(expOutXLFile))
def test_labelConv32bitTo16bit():
"""
Testing the function FarsightOPConv.img32bit16bitIO.labelConv32bitTo16bit
"""
test32BitFile = os.path.join(
"tests", "files",
"Act5C_no5_med1_C428_dec1_label_corrected32Bit_13LabelSubset.tif")
img32bit = tifffile.imread(test32BitFile)
imgs16Bit, labelMap = labelConv32bitTo16bit(img32bit)
assert len(imgs16Bit) == 3
opImgBase = os.path.join("tests", "files", "funcs",
"labelConv32bitTo16bit", "outputImg")
expOPImageFiles = [f"{opImgBase}_{ind:d}_exp.tif" for ind in range(3)]
expLabelMapXL = os.path.join("tests", "files", "funcs",
"labelConv32bitTo16bit",
"outputLabelMap_exp.xlsx")
expLabelMapDF = pd.read_excel(expLabelMapXL)
assert expLabelMapDF.equals(labelMap.astype(np.int64))
for expOPImageFile, opImg in zip(expOPImageFiles, imgs16Bit):
expOPImage = tifffile.imread(expOPImageFile)
assert np.allclose(expOPImage, opImg)
def test_getLabelShapeStats():
"""
Testing the function FarsightOPConv.sitkFuncs.getLabelShapeStatistics
"""
testFile = os.path.join(
"tests", "files",
"Act5C_no5_med1_C428_dec1_label_20LabelSubset_corrected32Bit_exp.tiff")
outFile = os.path.join("tests", "files", "funcs", "getLabelShapeStats",
"output.xlsx")
expected_outFile = os.path.join("tests", "files", "funcs",
"getLabelShapeStats",
"expectedOutput.xlsx")
testImageNP = tifffile.imread(testFile)
testImageNPUInt16 = testImageNP.astype(np.uint16)
measureNames, measureValues = getLabelShapeStatistics(testImageNPUInt16)
outDF = pd.DataFrame(columns=measureNames, data=measureValues)
outDF.to_excel(outFile)
expected_outDF = pd.read_excel(expected_outFile)
arrayCols = ["Centroid", "Principal Moments"]
expected_outDF[arrayCols] = expected_outDF[arrayCols].applymap(make_tuple)
assert outDF.equals(expected_outDF)
def __init__(self, outputlabelImageFile:str, outputSeedsTXT: str):
"""
Initializes the object by reading in output label image and seeds
:param outputLabelImageFile: string, path of the output label image file generated by farsight
:param outputSeedsTXT: string, path of the output seed text file generated by farsight
"""
self.outputlabelImageFile = outputlabelImageFile
self.outputSeedsTXT = outputSeedsTXT
self.seeds = np.loadtxt(self.outputSeedsTXT, dtype=int)
self.labelImage = tifffile.imread(self.outputlabelImageFile)