Beispiel #1
0
def test():
    """Test Stiching module"""
    import ClearMap.Alignment.Stitching as st
    reload(st)

    st.printSettings()
    
    from ClearMap.Settings import ClearMapPath;
    import os
    
    datadir = os.path.join(ClearMapPath, 'Test/Data/Stitching');
    outdir = os.path.join(ClearMapPath,  'Test/Data/Stitching/Output');
    
    #import glob
    #fn = os.path.join(datadir, '14-22-21_TH-s3-ov45-na004_UltraII[[]* x *[]]_C00_xyz-Table Z*.ome.tif')
    #fn = os.path.join(datadir, '*')
    #print fn
    #print glob.glob(fn)
    
    fileExpression = os.path.join(datadir, r'14-22-21_TH-s3-ov45-na004_UltraII\[(?P<row>\d{2}) x (?P<col>\d{2})\]_C00_xyz-Table Z(?P<z>\d{4}).ome.tif')
    
    st.findFileList(fileExpression)
    
    ff = st.findFirstFile(fileExpression, sort = False)
    
    fi = st.findFileInfo(ff);
    print fi
    
    ### import file
    reload(st); 
    #xmlstring = st.xmlImportFile(fileExpression, overlap = None, origin = None, resolution = None, tiling = None, tileExpression = None, zRange = None, xmlImportFile = None, asString = True)
    #print xmlstring
    
    importfile = st.xmlImportFile(fileExpression, xmlImportFile = os.path.join(datadir, 'TeraStitcher_import.xml'));
    print importfile

    ### run import
    st.importData(importfile)
    
    ### preview
    st.plotImportPreview(importfile)
    
    ### run alignment chain
    reload(st)
    alignfile = st.alignData(importfile, slices = 5, search = (10,10,0), xmlResultFile = os.path.join(datadir, 'TeraStitcher_align.xml'));

    ### project
    reload(st);
    projectfile = st.projectDisplacements(alignfile,  xmlResultFile = os.path.join(datadir, 'TeraStitcher_project.xml'))
    
    
    ### threshold
    reload(st);
    thresfile = st.thresholdDisplacements(projectfile,  xmlResultFile = os.path.join(datadir, 'TeraStitcher_threshold.xml'))

    ### place
    reload(st);
    placefile = st.placeTiles(thresfile, xmlResultFile = os.path.join(datadir, 'TeraStitcher_place.xml'))
    
    ### stitch it
    reload(st);
    result = st.stitchData(placefile, resultPath = os.path.join(datadir, 'stiched.tif'))
    result = st.stitchData(placefile, resultPath = os.path.join(datadir, 'stiched.tif'))
def test():
    """Test Stiching module"""
    import ClearMap.Alignment.Stitching as st

    reload(st)

    st.printSettings()

    from ClearMap.Settings import ClearMapPath
    import os

    datadir = os.path.join(ClearMapPath, "Test/Data/Stitching")
    outdir = os.path.join(ClearMapPath, "Test/Data/Stitching/Output")

    # import glob
    # fn = os.path.join(datadir, '14-22-21_TH-s3-ov45-na004_UltraII[[]* x *[]]_C00_xyz-Table Z*.ome.tif')
    # fn = os.path.join(datadir, '*')
    # print fn
    # print glob.glob(fn)

    fileExpression = os.path.join(
        datadir,
        r"14-22-21_TH-s3-ov45-na004_UltraII\[(?P<row>\d{2}) x (?P<col>\d{2})\]_C00_xyz-Table Z(?P<z>\d{4}).ome.tif",
    )

    st.findFileList(fileExpression)

    ff = st.findFirstFile(fileExpression, sort=False)

    fi = st.findFileInfo(ff)
    print fi

    ### import file
    reload(st)
    # xmlstring = st.xmlImportFile(fileExpression, overlap = None, origin = None, resolution = None, tiling = None, tileExpression = None, zRange = None, xmlImportFile = None, asString = True)
    # print xmlstring

    importfile = st.xmlImportFile(fileExpression, xmlImportFile=os.path.join(datadir, "TeraStitcher_import.xml"))
    print importfile

    ### run import
    st.importData(importfile)

    ### preview
    st.plotImportPreview(importfile)

    ### run alignment chain
    reload(st)
    alignfile = st.alignData(
        importfile, slices=5, search=(10, 10, 0), xmlResultFile=os.path.join(datadir, "TeraStitcher_align.xml")
    )

    ### project
    reload(st)
    projectfile = st.projectDisplacements(alignfile, xmlResultFile=os.path.join(datadir, "TeraStitcher_project.xml"))

    ### threshold
    reload(st)
    thresfile = st.thresholdDisplacements(
        projectfile, xmlResultFile=os.path.join(datadir, "TeraStitcher_threshold.xml")
    )

    ### place
    reload(st)
    placefile = st.placeTiles(thresfile, xmlResultFile=os.path.join(datadir, "TeraStitcher_place.xml"))

    ### stitch it
    reload(st)
    result = st.stitchData(placefile, resultPath=os.path.join(datadir, "stiched.tif"))
    result = st.stitchData(placefile, resultPath=os.path.join(datadir, "stiched.tif"))
# -*- coding: utf-8 -*-
"""
Created on Fri Jul  8 17:11:51 2016
"""    
    
    
import ClearMap.Alignment.Stitching as st
reload(st)

st.printSettings()


import os


datadir = '/home/mtllab/Documents/th/cropped';
#datadir = '/home/mtllab/Documents/th/160412_mosaic_15-20-19';
outdir = '/home/mtllab/Documents/th/stitched';

#import glob
#fn = os.path.join(datadir, '14-22-21_TH-s3-ov45-na004_UltraII[[]* x *[]]_C00_xyz-Table Z*.ome.tif')
#fn = os.path.join(datadir, '*')
#print fn
#print glob.glob(fn)

#fileExpression = os.path.join(datadir, r'15-20-19_mosaic_UltraII\[(?P<row>\d{2}) x (?P<col>\d{2})\]_C00_xyz-Table Z(?P<z>\d{4}).ome.tif')
fileExpression = os.path.join(datadir, r'15-20-19_mosaic_UltraII_(?P<row>\d{2})_x_(?P<col>\d{2})_C00_xyz-Table Z(?P<z>\d{4}).ome.tif')

#st.findFileList(fileExpression)

ff = st.findFirstFile(fileExpression, sort = True)

import ClearMap.Settings as settings

import ClearMap.Alignment.Stitching as st

import os

import numpy as np


datadir ='/home/mtllab/Documents/th/';

fn = os.path.join(datadir, r'160412_mosaic_15-20-19/15-20-19_mosaic_UltraII\[(?P<row>\d{2}) x (?P<col>\d{2})\]_C00_xyz-Table Z(?P<z>\d{4}).ome.tif')

_, gr = st.findFileList(fn , sort = True, groups = ['row','col'], absolute = True)
groups = [];
for i in range(gr.shape[1]):
    groups.append(np.unique(gr[:,i]));

print groups

for i in groups[0]:
    for j in groups[1]:
        fileExpression = os.path.join(datadir, r'160412_mosaic_15-20-19/15-20-19_mosaic_UltraII\[%s x %s]_C00_xyz-Table Z\d{4}.ome.tif' % (i,j))

        io.dataSize(fileExpression)

        io.readMetaData(fileExpression, info = ['size', 'overlap', 'resolution'])