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'])