Commit 22f61511 authored by Martin Schorb's avatar Martin Schorb
Browse files

many updates to doc and applications

parent b2513064
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
......@@ -122,7 +122,7 @@ def virtmapfrompoint(acq_item,idx,allitems,maps,targetitem,target_merge,resultli
prefix = 'V_'
newnavitem['Acquire'] = ['0']
elif targetitem['MapLDConSet'] == ['4']:
#newnavitem['Acquire'] = ['1']
newnavitem['Acquire'] = ['0']
prefix = 'P_'
else:
prefix='m_'
......
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
......@@ -509,7 +509,7 @@ def map_matrix(mapitem):
# -------------------------------
#%%
def mergemap(mapitem,crop=False,black=False,blendmont=True):
def mergemap(mapitem,crop=False,black=False,blendmont=True,bigstitch=False):
#%%
# processes a map item and merges the mosaic using IMOD
# generates a dictionary with metadata for this procedure
......@@ -836,21 +836,21 @@ def mergemap(mapitem,crop=False,black=False,blendmont=True):
tileloc = numpy.array([tpx / xstep,tpy/ystep]).T
# if not blendmont:
# #prepare coordinate list for Big Stitcher
# print('preparing coordinate list for BigStitcher for map item '+mapitem['# Item']+'.')
# outpx = tilepx.copy()
if not blendmont and bigstitch:
#prepare coordinate list for Big Stitcher
print('preparing coordinate list for BigStitcher for map item '+mapitem['# Item']+'.')
outpx = tilepx.copy()
# stitchname = mapfile+'.stitch.csv'
# stitchfile = open(stitchname,'w')
stitchname = mapfile+'.stitch.csv'
stitchfile = open(stitchname,'w')
# stitchfile.write('dim=2\n')
# #stitchfile.write('ViewSetupID;TimePointID;(position_x, position_y, position_z)\n')
stitchfile.write('dim=2\n')
#stitchfile.write('ViewSetupID;TimePointID;(position_x, position_y, position_z)\n')
# for j,item in enumerate(outpx):
# stitchfile.write(str(j)+";;"+"(%s, %s" % (int(item[0]),-int(item[1]))+")\n")
for j,item in enumerate(outpx):
stitchfile.write(str(j)+";;"+"(%s, %s" % (int(item[0]),-int(item[1]))+")\n")
# stitchfile.close()
stitchfile.close()
m['sections'] = numpy.array(list(map(int,tileloc[:,0]*m['frames'][1]+tileloc[:,1])))
......
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
File mode changed from 100755 to 100644
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment