def load_data(self, loadPath, imFile, refFile = None, plotting = False):
""" Load data into the class from file
"""
import loadDataToNumpy_class
ld_image = loadDataToNumpy_class.loadInDataToNumpy(loadPath + imFile)
self.im = ld_image.loadData()
self.imShape = np.shape(self.im)
if refFile is not None:
ld_image = loadDataToNumpy_class.loadInDataToNumpy(loadPath + refFile)
self.ref = ld_image.loadData()
self.refExists = True
else:
self.refExists = False
if plotting:
self.plot_raw_input()
def __init__(self, filePath):
# The input is the whole file path
self.filePath = filePath
self.fileIdentifier = self.filePath.split("/")[-1].split("_")[0]
ld = loadDataToNumpy_class.loadInDataToNumpy(filePath)
self.im_raw = ld.loadData()
def loadData(self, filePath, line_of_pchannel, width_pchannel):
import loadDataToNumpy_class
ld = loadDataToNumpy_class.loadInDataToNumpy(filePath)
self.im = ld.loadData()
self.imShape = np.shape(self.im)
self.line_of_pchannel = line_of_pchannel
self.width_pchannel = width_pchannel
def load_data(self, loadPath, phaseFile, plotting = False):
import loadDataToNumpy_class
ld_image = loadDataToNumpy_class.loadInDataToNumpy(loadPath + phaseFile)
self.phase = ld_image.loadData()
self.phaseShape = np.shape(self.phase)
if plotting:
plt.pcolormesh(self.phase)
plt.colorbar()
plt.show()
def test_findRotation(self):
filePath = "/Volumes/GoogleDrive/My Drive/Experimental_Codes/Interferometry_Data_Extraction/Test_Data/"
fileName = filePath + "SyntheticReference.tiff"
testData = loadDataToNumpy_class.loadInDataToNumpy(fileName)
d = testData.loadData()
rot = rotateArray.rotateFringesToVertical(d)
rotation = rot.findRotation(startIndex = 0, numberOfLineouts = 15,
horzStart = 100, horzEnd = 500)
print ("Angle in Degrees", rotation)
print ("Expected Angle ", 0)
self.assertAlmostEqual(rotation, 0, places = 5)
def LoadData(self, fileName):
""" Load the data using the class
"""
import loadDataToNumpy_class
ld = loadDataToNumpy_class.loadInDataToNumpy(fileName)
self.im = ld.loadData()
self.shape = np.shape(self.im)
if self.plotting:
plt.imshow(self.im, vmin = np.average(self.im) - (self.im.max() - np.average(self.im)))
plt.colorbar()
plt.show()
def test_loading_txt(self):
#
rootExperimentFolder = "/Volumes/GoogleDrive/My Drive/2019 RR Analysis/BG_sub_Rot_F2Vert/"
filePath = rootExperimentFolder + "cropROI20190211r008s103.txt"
ld = loadDataToNumpy_class.loadInDataToNumpy(filePath)
im =ld.loadData()
typeName = str(type(im))
ndarray = False
if "ndarray" in typeName:
ndarray = True
self.assertEqual(ndarray, True)
def test_loading_tiff(self):
#
rootExperimentFolder = "/Volumes/GoogleDrive/Shared drives/Murphy Group/GeminiRR_2019/"
filePath = rootExperimentFolder + "20190208/20190208r011/20190208r011s001_Probe_Interfero.tiff"
ld = loadDataToNumpy_class.loadInDataToNumpy(filePath)
im =ld.loadData()
typeName = str(type(im))
ndarray = False
if "ndarray" in typeName:
ndarray = True
self.assertEqual(ndarray, True)
def load_data(self, filePath, plotting=False):
import loadDataToNumpy_class
ld = loadDataToNumpy_class.loadInDataToNumpy(filePath)
self.phase = ld.loadData()
self.phaseShape = np.shape(self.phase)
if plotting:
plt.figure(figsize=(8, 4))
plt.title("Input phase")
plt.imshow(self.phase,
cmap=plt.cm.seismic,
norm=func.MidpointNormalize(midpoint=0))
plt.colorbar()
plt.show()
def loadReference(self, filepath, plotting = False):
ld = loadDataToNumpy_class.loadInDataToNumpy(filepath)
self.ref = ld.loadData()
if plotting:
plt.imshow(self.ref); plt.colorbar(); plt.title("Reference Image")
plt.show()
plt.imshow(im)
plt.show()
def lin(x, *params):
# linear fit function
m = params[0]
c = params[1]
return x *m + c
if __name__ == "__main__":
# Load the data
import loadDataToNumpy_class
rootExperimentFolder = "/Volumes/GoogleDrive/Shared drives/Murphy Group/GeminiRR_2019/"
filePath = rootExperimentFolder + "20190208/20190208r011/20190208r011s001_Probe_Interfero.tiff"
ld = loadDataToNumpy_class.loadInDataToNumpy(filePath)
im_raw = ld.loadData()
plotImage(im_raw, "Raw Data")
# Run the rotateArray class
rotAnal = rotateFringesToVertical(im_raw)
angle = rotAnal.findRotation(startIndex = 5, endIndex = 200,
plotting = True)
# print (angle)
rotatedImage = rotAnal.applyRotation(angle)
savePath = "/Volumes/GoogleDrive/My Drive/Experimental_Codes/Interferometry_Data_Extraction/"
np.savetxt(savePath + "verticalFrings.txt", rotatedImage)