Python Plot.plotOverlayLabel Examples

Example #1

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)
from ClearMap.ImageProcessing.Filter.DoGFilter import filterDoG
dataDoG = filterDoG(dataBGR, size=(8, 8, 4), verbose=True)
from ClearMap.ImageProcessing.MaximaDetection import findExtendedMaxima
dataMax = findExtendedMaxima(dataDoG, hMax=None, verbose=True, threshold=10)
from ClearMap.ImageProcessing.MaximaDetection import findCenterOfMaxima
cells = findCenterOfMaxima(data, dataMax)
from ClearMap.ImageProcessing.CellSizeDetection import detectCellShape
dataShape = detectCellShape(dataDoG, cells, threshold=15)
plt.plotOverlayLabel(dataDoG / dataDoG.max(), dataShape, z=(10, 16))

Example #2

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)
from ClearMap.ImageProcessing.Filter.DoGFilter import filterDoG
dataDoG = filterDoG(dataBGR, size=(8, 8, 4), verbose=True)
from ClearMap.ImageProcessing.MaximaDetection import findExtendedMaxima
dataMax = findExtendedMaxima(dataDoG, hMax=None, verbose=True, threshold=10)
plt.plotOverlayLabel(dataDoG / dataDoG.max(),
                     dataMax.astype('int'),
                     z=(10, 16))

Example #3

File: cellvisualization2.py Project: alexcwsmith/imageProcessing

                               dataBGR_write,
                               fileRange,
                               pointColor=None)
io.writeData(os.path.join(BaseDirectory, 'cells_check.tif'), data)

#DoG Filter
from ClearMap.ImageProcessing.Filter.DoGFilter import filterDoG
dataDoG = filterDoG(dataBGR, size=(7, 7, 9), verbose=False)
plt.plotTiling(dataDoG, inverse=True, x=(600, 700), y=(600, 700), z=(1, 15))

#Find Extended Maxima
from ClearMap.ImageProcessing.MaximaDetection import findExtendedMaxima
dataMax = findExtendedMaxima(dataDoG, hMax=None, verbose=True, threshold=500)
plt.plotOverlayLabel(dataDoG / dataDoG.max(),
                     dataMax.astype('int'),
                     x=(1750, 1850),
                     y=(1050, 1150),
                     z=(1, 9))

#Find Peak Intensity
findIntensityParameter = {
    "method":
    'Max',  # (str, func, None)   method to use to determine intensity (e.g. "Max" or "Mean") if None take intensities at the given pixels
    "size": (
        7, 7, 5
    )  # (tuple)             size of the search box on which to perform the *method*
}
#Cell Shape Parameters
detectCellShapeParameter = {
    "threshold":
    500,  # (float or None)      threshold to determine mask. Pixels below this are background if None no mask is generated

Example #4

File: docs_script.py Project: ChristophKirst/ClearMap

from ClearMap.ImageProcessing.MaximaDetection import findExtendedMaxima
dataMax = findExtendedMaxima(dataDoG, hMax = None, verbose = True, threshold = 10);
#plt.plotOverlayLabel(  dataDoG / dataDoG.max(), dataMax.astype('int'), z = (10,16))



from ClearMap.ImageProcessing.MaximaDetection import findCenterOfMaxima
cells = findCenterOfMaxima(data, dataMax);
print cells.shape

plt.plotOverlayPoints(data, cells, z = (10,16))


from ClearMap.ImageProcessing.CellSizeDetection import detectCellShape        
dataShape = detectCellShape(dataDoG, cells, threshold = 15);
plt.plotOverlayLabel(dataDoG / dataDoG.max(), dataShape, z = (10,16))


# find intensities / cell sizes
from ClearMap.ImageProcessing.CellSizeDetection import findCellSize, findCellIntensity

#size of cells        
cellSizes = findCellSize(dataShape, maxLabel = cells.shape[0]);

#intensity of cells
cellIntensities = findCellIntensity(dataBGR, dataShape,  maxLabel = cells.shape[0]);

 
import matplotlib.pyplot as mpl 

mpl.figure()

Example #5

File: imageanalysis-8.py Project: ChristophKirst/ClearMap

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);
from ClearMap.ImageProcessing.Filter.DoGFilter import filterDoG
dataDoG = filterDoG(dataBGR, size=(8,8,4), verbose = True);
from ClearMap.ImageProcessing.MaximaDetection import findExtendedMaxima
dataMax = findExtendedMaxima(dataDoG, hMax = None, verbose = True, threshold = 10);
plt.plotOverlayLabel(dataDoG / dataDoG.max(), dataMax.astype('int'), z = (10,16), x = (50,100), y = (50,100))