def test():
"""Test voxelization module"""
import ClearMap.Analysis.Voxelization as self
reload(self)
import ClearMap.Analysis.VoxelizationCode as vox
import numpy
points = numpy.random.rand(200,3) * 10;
#use cython code
vi = vox.voxelizeSphere(points, 20,20,20, 5,5,5);
import ClearMap.Visualization.Plot as Plot
Plot.plotTiling(vi)
#use voxelize
vi = self.voxelize(points, dataSize = (20,20,20), size = (5,5,5));
Plot.plotTiling(vi)
#weighted voxelization
points = numpy.random.rand(10,3) * 10;
weights = numpy.random.rand(10);
#use voxelize
vi = self.voxelize(points, dataSize = (20,20,20), size = (5,5,5));
viw = self.voxelize(points, dataSize = (20,20,20), size = (5,5,5), weights = weights);
Plot.plotTiling(vi)
Plot.plotTiling(viw)
def plotImportPreview(importResult):
"""Plots the prestiched preview file to check orientations and coarse alignment
Arguments:
importResult (str): the base directory of the image data or the import xml file
Returns:
object: plot axes
"""
return cplt.plotTiling(readImportPreview(importResult));
def plotImportPreview(importResult):
"""Plots the prestiched preview file to check orientations and coarse alignment
Arguments:
importResult (str): the base directory of the image data or the import xml file
Returns:
object: plot axes
"""
return cplt.plotTiling(readImportPreview(importResult))
def test():
"""Test the statistics array"""
import ClearMap.Analysis.Statistics as self
reload(self)
import numpy, os
import matplotlib.pyplot as plt
#x = stats.norm.rvs(loc=5,scale=1,size=1500)
#y = stats.norm.rvs(loc=-5,scale=1,size=1500)
s = numpy.ones((5, 4, 20))
s[:, 0:3, :] = -1
x = numpy.random.rand(4, 4, 20)
y = numpy.random.rand(5, 4, 20) + s
# print stats.ttest_ind(x,y, axis = 0, equal_var = False);
pvals, psign = self.tTestVoxelization(x, y, signed=True)
print pvals
pvalscol = self.colorPValues(pvals,
psign,
positive=[255, 0, 0],
negative=[0, 255, 0])
import ClearMap.Visualization.Plot as plt_cm
plot = plt_cm.plotTiling(pvalscol)
plt.show()
# test points
basedir = '/home/vzickus/repos/ClearMap-Debug/ClearMap'
import ClearMap.Settings as settings
pf = os.path.join(basedir,
'Test/Synthetic/cells_transformed_to_reference.csv')
pf = numpy.loadtxt(pf, delimiter=',')
pg = (pf, pf)
pc = self.countPointsGroupInRegions(pg)
pvals, tvals = self.tTestPointsInRegions(pg, pg, signed=True)
import os
import ClearMap.Settings as settings
filename = os.path.join(settings.ClearMapPath, 'Test/Data/ImageAnalysis/cfos-substack.tif');
import ClearMap.Visualization.Plot as plt
import ClearMap.IO as io
data = io.readData(filename, z = (0,26));
import ClearMap.ImageProcessing.BackgroundRemoval as bgr
dataBGR = bgr.removeBackground(data.astype('float'), size=(3,3), verbose = True);
plt.plotTiling(dataBGR, inverse = True, z = (10,16));
import os
import ClearMap.Settings as settings
filename = os.path.join(settings.ClearMapPath,
'Test/Data/ImageAnalysis/cfos-substack.tif')
import ClearMap.Visualization.Plot as plt
import ClearMap.IO as io
data = io.readData(filename, z=(0, 26))
plt.plotTiling(data, x=(0, 70), y=(0, 50), z=(10, 16))
# -*- coding: utf-8 -*-
"""
Created on Sat Dec 19 04:29:29 2015
@author: ckirst
"""
import os
import ClearMap.Settings as settings
filename = os.path.join(settings.ClearMapPath,
'Test/Data/ImageAnalysis/cfos-substack.tif')
import ClearMap.Visualization.Plot as plt
import ClearMap.IO as io
data = io.readData(filename, z=(0, 30))
plt.plotTiling(data, inverse=True, z=(10, 16))
#import ClearMap.ImageProcessing.ImageStatistics as stat
#stat.calculateStatistics(filename, method = 'mean', verbose = True)
import ClearMap.ImageProcessing.BackgroundRemoval as bgr
dataBGR = bgr.removeBackground(data.astype('float'),
size=(10, 10),
verbose=True)
plt.plotTiling(dataBGR, inverse=True, z=(10, 16))
from ClearMap.ImageProcessing.Filter.DoGFilter import filterDoG
dataDoG = filterDoG(dataBGR, size=(8, 8, 4), verbose=True)
plt.plotTiling(dataDoG, inverse=True, z=(10, 16))
import os
import os import ClearMap.Settings as settings filename = os.path.join(settings.ClearMapPath, 'Test/Data/ImageAnalysis/cfos-substack.tif'); import ClearMap.Visualization.Plot as plt import ClearMap.IO as io data = io.readData(filename, z = (0,26)); plt.plotTiling(data, x= (0,70), y = (0,50), z = (10,16));
import ClearMap.Settings as settings
import ClearMap.Visualization.Plot as plt
import ClearMap.ImageProcessing.BackgroundRemoval as bgr
import matplotlib as mplt
BaseDirectory = '/d2/studies/ClearMap/IA_iDISCO/IA1_RB/'
filename = os.path.join(BaseDirectory, 'IA1_RB_cfos_stack.ome.tif')
data = io.readData(filename, z=(600, 650))
# size restriction
fileRange = 'x = (1050, 1350), y = (550,850), z = (25,34)'
""" note that the Z coordinate in fileRange variable are relative to the planes imported in the data variable.
So in this case, you would be imaging planes 675-684.
"""
plt.plotTiling(data, inverse=True, x=(1250, 1350), y=(550, 650), z=(25, 34)) #
# background subtraction
dataBGR = bgr.removeBackground(data.astype('float'),
size=(5, 5),
verbose=False,
save=None)
dataBGR_write = plt.plotTiling(dataBGR,
inverse=True,
x=(1250, 1350),
y=(550, 650),
z=(25, 34))
dataBGR_write = plt.overlayPoints(dataBGR, fileRange)
mplt.pyplot.savefig(os.path.join(BaseDirectory, 'dataBGR_write.tif'))
io.writeData(os.path.join(BaseDirectory, 'background_8.tif'), dataBGR_write)
io.writeData(os.path.join(BaseDirectory, 'cells_check.tif'), data)
import os import ClearMap.Settings as settings filename = os.path.join(settings.ClearMapPath, 'Test/Data/ImageAnalysis/cfos-substack.tif'); import ClearMap.Visualization.Plot as plt import ClearMap.IO as io data = io.readData(filename, z = (0,26)); plt.plotTiling(data);