def IntensityFrame2(self):
buf, att = im7.readim7(self.s)
frame1 = buf.get_frame(1)
bfunc = np.vectorize(lambda a, b: a if a>=b else 0)
binarize_frame1 = bfunc(frame1, mahotas.thresholding.otsu(frame1))
buf.delete()
att.delete()
return str(np.mean(binarize_frame1))
#Copyright (C) 2010 Fabricio Silva
"""
"""
import sys
sys.path.append('..')
import numpy as np
trace = True
flags = [True, True, True, True]
if trace:
import matplotlib.pyplot as plt
# Figure1 : vx, 2:vy, 3:vz
f1 = plt.figure(1)
ax = f1.add_subplot(111)
nx, ny = 118, 78
d = {'interpolation':'nearest', 'vmin':-10, 'vmax':10, 'origin':'upper'}
# libim7
if flags[0]:
import libim7 as im7
buf1, att1 = im7.readim7('PTV_B00013.VC7')
dx = {}#'extent':(buf1.x[0],buf1.x[-1],buf1.y[0],buf1.y[-1])}
dx.update(d)
if trace:
ax.quiver(buf1.x, buf1.y, buf1.vx, buf1.vy, np.sqrt(buf1.vx**2+buf1.vy**2),
scale=1.5)
if trace:
plt.show()
@author: rahmann
"""
import glob
import numpy as np
from os import path
from libim7 import readim7
im7_folder = "E:\\DaVisProjects\\DaVis10_IJ_Sept2019\\IJ\\0p30\\5Passes_5x5 Gaussian smoothing filter\\MaskOutImage\\" + \
"AddCameraAttributes\\AddAttributes\\CompressExpand\\Mult\\MART_(iterations=1000,smooth=0.5,1000,sparse=0)\\Data\\S00001\\"
im7_files = glob.glob(im7_folder + "*.im7")
for n, im7_file in enumerate(im7_files):
buf, att = readim7(im7_file)
if n == 0:
# Number of voxels in X, Y, Z
nx = buf.nx
ny = buf.ny
nz = len(im7_files)
volume = np.zeros((nx, ny, nz))
volume[:, :, n] = buf.blocks.T[:, :, 0]
# Millimeters per voxel from calibration
scale_x = float(att['_SCALE_X'].rsplit(' ')[0])
scale_y = float(att['_SCALE_Y'].rsplit(' ')[0])
scale_z = float(att['_SCALE_Z'].rsplit(' ')[0])
# Figure1 : vx, 2:vy, 3:vz
f1 = plt.figure(1)
ax0 = f1.add_subplot(211)
ax1 = f1.add_subplot(212)
lAxs = (ax0, ax1)
d = {
'interpolation':'nearest',
# 'vmin':-10, 'vmax':10,
'origin':'upper',
'aspect':'auto'}
lBuf = []
for ind, ext in enumerate(lExt[::-1]):
fname = __file__.replace(".py", ext)
buf1, att1 = im7.readim7(fname)
lBuf.append(buf1)
dx = {'extent':(buf1.x[0],buf1.x[-1],buf1.y[0],buf1.y[-1])}
dx.update(d)
if trace:
im = lAxs[ind].imshow(buf1.get_frame(0), **dx)
lAxs[ind].text(.02, .02, fname, transform=lAxs[ind].transAxes)
lAxs[ind].set_xlabel(buf1.scaleX.description.replace('\n',' ')+buf1.scaleX.unit)
lAxs[ind].set_ylabel(buf1.scaleY.description.replace('\n',' ')+buf1.scaleY.unit)
cb = plt.colorbar(im, ax = lAxs[ind])
cb.set_label(buf1.scaleI.description.replace('\n',' ')+buf1.scaleI.unit)
if trace:
plt.savefig(__file__.replace('.py', '.pdf'))
plt.close('all')
#plt.show()
f1 = plt.figure(1)
ax0 = f1.add_subplot(211)
ax1 = f1.add_subplot(212)
lAxs = (ax0, ax1)
d = {
'interpolation': 'nearest',
# 'vmin':-10, 'vmax':10,
'origin': 'upper',
'aspect': 'auto'
}
lBuf = []
for ind, ext in enumerate(lExt[::-1]):
fname = __file__.replace(".py", ext)
buf1, att1 = im7.readim7(fname)
lBuf.append(buf1)
dx = {'extent': (buf1.x[0], buf1.x[-1], buf1.y[0], buf1.y[-1])}
dx.update(d)
if trace:
im = lAxs[ind].imshow(buf1.get_frame(0), **dx)
lAxs[ind].text(.02, .02, fname, transform=lAxs[ind].transAxes)
lAxs[ind].set_xlabel(
buf1.scaleX.description.replace('\n', ' ') + buf1.scaleX.unit)
lAxs[ind].set_ylabel(
buf1.scaleY.description.replace('\n', ' ') + buf1.scaleY.unit)
cb = plt.colorbar(im, ax=lAxs[ind])
cb.set_label(
buf1.scaleI.description.replace('\n', ' ') + buf1.scaleI.unit)
if trace:
plt.savefig(__file__.replace('.py', '.pdf'))
# Figure1 : vx, 2:vy, 3:vz
f1 = plt.figure(1)
f2 = plt.figure(2)
f3 = plt.figure(3)
f1.suptitle('$V_x$')
f2.suptitle('$V_y$')
f3.suptitle('$V_z$')
Ax = [f.add_subplot(221) for f in (f1, f2, f3)]
share = lambda ind: {'sharex': Ax[ind - 1], 'sharey': Ax[ind - 1]}
nx, ny = 118, 78
d = {'interpolation': 'nearest', 'vmin': -10, 'vmax': 10, 'origin': 'lower'}
# libim7
if flags[0]:
import libim7 as im7
buf1, att1 = im7.readim7('SOV2_01_100_davis.VC7')
dx = {'extent': (buf1.x[0], buf1.x[-1], buf1.y[0], buf1.y[-1])}
dx.update(d)
if trace:
Ax[0].imshow(buf1.vx.T, **dx)
Ax[1].imshow(buf1.vy.T, **dx)
Ax[2].imshow(buf1.vz.T, **dx)
Ax[0].text(.02, .02, 'VC7', transform=Ax[0].transAxes)
# txt: comma to dot
if flags[1]:
f = file('SOV2_01_100_davis.txt', 'r')
f.readline()
string = f.read()
f.close()
string = string.replace(',', '.')
# Figure1 : vx, 2:vy, 3:vz
f1 = plt.figure(1)
f2 = plt.figure(2)
f3 = plt.figure(3)
f1.suptitle('$V_x$')
f2.suptitle('$V_y$')
f3.suptitle('$V_z$')
Ax = [f.add_subplot(221) for f in (f1,f2,f3)]
share = lambda ind: {'sharex': Ax[ind-1], 'sharey':Ax[ind-1]}
nx, ny = 118, 78
d = {'interpolation':'nearest', 'vmin':-10, 'vmax':10, 'origin':'lower'}
# libim7
if flags[0]:
import libim7 as im7
buf1, att1 = im7.readim7('SOV2_01_100_davis.VC7')
dx = {'extent':(buf1.x[0],buf1.x[-1],buf1.y[0],buf1.y[-1])}
dx.update(d)
if trace:
Ax[0].imshow(buf1.vx.T, **dx)
Ax[1].imshow(buf1.vy.T, **dx)
Ax[2].imshow(buf1.vz.T, **dx)
Ax[0].text(.02, .02, 'VC7', transform=Ax[0].transAxes)
# txt: comma to dot
if flags[1]:
f = file('SOV2_01_100_davis.txt', 'r')
f.readline(); string = f.read(); f.close(); string = string.replace(',', '.')
buf2 = np.fromstring(string, sep='\t').reshape((ny,nx,5))
x, y = buf2[:,:,0][0,:], buf2[:,:,1][:,0]
dx = {'extent':(x[0],x[-1],y[0],y[-1])}
def __init__(self, path):
self.path = path.split("/")
self.s = path
if path:
self.buffer, self.attr = im7.readim7(self.s)
"""
"""
import sys
sys.path.append('../libim7')
import numpy as np
trace = False
flags = [True, True, True, True]
if trace:
import matplotlib.pyplot as plt
# Figure1 : vx, 2:vy, 3:vz
f1 = plt.figure(1)
ax = f1.add_subplot(111)
nx, ny = 118, 78
d = {'interpolation':'nearest', 'vmin':-10, 'vmax':10, 'origin':'upper'}
# libim7
if flags[0]:
import libim7 as im7
buf1, att1 = im7.readim7('PTV_B00013.VC7')
dx = {}#'extent':(buf1.x[0],buf1.x[-1],buf1.y[0],buf1.y[-1])}
dx.update(d)
if trace:
ax.quiver(buf1.x, buf1.y, buf1.vx, buf1.vy, np.sqrt(buf1.vx**2+buf1.vy**2),
scale=1.5)
if trace:
plt.savefig(__file__.replace('.py', '.pdf'))
plt.show()
