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Commit 558d3bb7 authored by Martin Schorb's avatar Martin Schorb
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add points on map function

parent a6631d27
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Showing with 57 additions and 145 deletions
pyEM.py
View file @ 558d3bb7
......@@ -54,7 +54,7 @@ p1 = Popen("imodinfo", shell=True, stdout=PIPE)
o=list()
for line in p1.stdout:
o.append(line)
if o == []:
print('Warning! - No IMOD installation found')
imod_ver = [0,0,0]
......@@ -242,24 +242,24 @@ def map_header(m):
if (type(m) is mrc.mrcfile.MrcFile) | (type(m) is mrc.mrcmemmap.MrcMemmap):
# extracts MRC header information for a given mrc.object (legacy from reading mrc headers)
header['xsize'] = numpy.int(m.header.nx)
header['ysize'] = numpy.int(m.header.ny)
header['stacksize'] = numpy.int(m.header.nz)
# determine the scale
header['pixelsize'] = m.voxel_size.x / 10000 # in um
elif (type(m) is dict):
if ("MapFile" in m.keys()):
if ("MapFile" in m.keys()):
merge = mergemap(m,blendmont=False)
header = merge['mapheader']
elif(type(m) is str):
if os.path.exists(m):
if os.path.splitext(m)[1] in mrcext:
header = map_header(mrc.mmap(m, permissive = 'True'))
return header
# -------------------------------
......@@ -568,11 +568,11 @@ def mergemap(mapitem,crop=False,black=False,blendmont=True):
maphead0 = mdoc_item(idoctxt,[],header=True)
im = list()
if montage_tiles == 0:
# stack of single images
mergefile = mapfile[:mapfile.find('.idoc')]+'{:04d}'.format(mapsection)+'.tif'
mergeheader['stacksize'] = 0
mergeheader['stacksize'] = 0
tilepos = mapitem['StageXYZ'][0:2]
tilepx = '0'
tilepx=numpy.array([[tilepx,tilepx,tilepx],[tilepx,tilepx,tilepx]])
......@@ -586,42 +586,42 @@ def mergemap(mapitem,crop=False,black=False,blendmont=True):
else:
if mdoc_item(idoctxt,'MontSection = 0') == []: #older mdoc file format, created before SerialEM 3.7x
print('Warning - item'+mapitem['# Item']+': Series of tif images without montage information. Assume pixel size is consistent for all sections.')
pixelsize = float(maphead0['PixelSpacing'][0])/ 10000 # in um
else:
mont_item = mdoc_item(idoctxt,'MontSection = '+str(mapsection))
pixelsize = float(mont_item['PixelSpacing'][0])/ 10000 # in um
for i in range(0,numpy.min([montage_tiles,stacksize])):
tilefile = mapfile[:mapfile.find('.idoc')]+'{:04d}'.format(mapsection + i)+'.tif'
im.append(tilefile)
tile = mdoc_item(idoctxt,'Image = '+os.path.basename(tilefile))
tilepos.append(tile['StagePosition'])
tilepx1.append(tile['PieceCoordinates'])
if 'AlignedPieceCoordsVS' in tile:
m['Sloppy'] = True
tilepx.append(tile['AlignedPieceCoordsVS'])
else:
tilepx.append(tile['AlignedPieceCoords'])
mergeheader['pixelsize'] = pixelsize
mapheader = mergeheader.copy()
mapheader['ysize'] = int(maphead0['ImageSize'][1])
mapheader['xsize'] = int(maphead0['ImageSize'][0])
imsz_x = int(maphead0['ImageSize'][0])
imsz_y = int(maphead0['ImageSize'][1])
overlapx = imsz_x - mapheader['xsize']
overlapy = imsz_y - mapheader['ysize']
# check if idoc is supported in IMOD (blendmont)
imod_vercheck = (imod_ver[0]>=4 and imod_ver[1]>=10 and imod_ver[2]>=42)
if blendmont:
mergebase = mbase + '_merged'+ '_s' + str(mapsection)
mergefile = mergebase+'.mrc'
......@@ -640,9 +640,9 @@ def mergemap(mapitem,crop=False,black=False,blendmont=True):
merge_mrc = mrc.mmap(mergefile, permissive = 'True')
im = merge_mrc.data
mergeheader = map_header(merge_mrc)
else:
mergeheader['xsize'] = int(tilepx[-1][0]) + mapheader['xsize']
mergeheader['ysize'] = int(tilepx[-1][1]) + mapheader['ysize']
......@@ -722,7 +722,7 @@ def mergemap(mapitem,crop=False,black=False,blendmont=True):
elif 'AlignedPieceCoords' in tile:
tilepx.append(tile['AlignedPieceCoords'])
else:
tilepx = tilepx1
tilepx = tilepx1
if mdoc_item(mdoclines,'MontSection = 0') == []: #older mdoc file format, created before SerialEM 3.7x
print('Warning: mrc stack without montage information. Assume pixel size is consistent for all sections.')
......@@ -1254,154 +1254,66 @@ def get_pixel(navitem,mergedmap,tile=False,outline=False):
# ------------------------------------------------------------
def ptsonmap(mapitem,pts):
# adds a point or polygon (pixel position) to a map and creates a navigator item from it
polynav=dict()
mapid = newID(nav,mapid+1)
def ptsonmap(mapitem,pts,nav):
# adds a point or polygon (pixel position) to a map and creates a navigator item from
# p is a list of numpy
print('Processing object '+ str(idx+1) + '/' + str(ntotal) + ' (%2.0f%%)' %(idx*100/ntotal) + ' at position %5u , %5u' %(c[0],c[1]))
mapid = mapitem['MapID']
p = pts[idx]
for p,idx in enumerate(pts):
im4, p4 = map_extract(im,c,p,px_scale,imsz1,maptf)
p = numpy.array(p)
polynav=dict()
if min(im4.shape) < 400:
print('Item is too close to border of map, skipping it.')
ntotal = ntotal - 1
continue
mheader = map_header(mapitem)
p4[:,1] = imsz1[0] - p4[:,1]
imsz1 = numpy.array([mheader['xsize'],mheader['ysize']])
cx = imsz1[1]
cy = imsz1[0]
px = numpy.array(numpy.transpose(p4[:,0]))
px = numpy.array2string(px,separator=' ')
px = px[2:-2]
p[:,1] = imsz1[0] - p[:,1]
py = numpy.array(numpy.transpose(p4[:,1]))
py = numpy.array2string(py,separator=' ')
py = py[2:-2]
if numpy.shape(p4)[0] == 1:
polynav['Type'] = ['0']
polynav['Color'] = ['0']
polynav['NumPts'] = ['1']
else:
polynav['Type'] = ['1']
polynav['Color'] = ['1']
polynav['NumPts'] = [str(p.shape[0])]
label = curr_map['# Item'] + '_' + str(idx).zfill(3)
idx = idx + 1
px = numpy.array(numpy.transpose(p[:,0]))
px = numpy.array2string(px,separator=' ')
px = px[2:-2]
imfile = 'virt_' + label + '.mrc'
py = numpy.array(numpy.transpose(p[:,1]))
py = numpy.array2string(py,separator=' ')
py = py[2:-2]
if os.path.exists(imfile): os.remove(imfile)
im5 = numpy.rot90(im4,3)
with mrc.new(imfile) as mrcf:
mrcf.set_data(im5.T)
mrcf.close()#
# map corner points
cx = imsz1[1]
cy = imsz1[0]
a = [[0,0],[cx,0],[cx,cy],[0,cy],[0,0]]
a = numpy.matrix(a) - [cx/2 , cy/2]
if numpy.shape(p)[0] == 1:
polynav['Type'] = ['0']
polynav['Color'] = ['0']
polynav['NumPts'] = ['1']
t_mat_i = numpy.linalg.inv(maptf)
c1 = a*t_mat_i
c_out = c.copy()
c_out[1] = imsz[0] - c_out[1]
# c1 = c1 + [c_out[0],c_out[1]]
# fill navigator
# map for realignment
newnavitem['MapFile'] = [imfile]
newnavitem.pop('StageXYZ','')
newnavitem.pop('RawStageXY','')
if curr_map['MapFramesXY'] == ['0', '0']:
newnavitem['CoordsInMap'] = [str(c_out[0]),str(c_out[1]),curr_map['StageXYZ'][2]]
else:
# newnavitem['CoordsInAliMont'] = [str(c_out[0]),str(c_out[1]),curr_map['StageXYZ'][2]]
# convert aligned pixel coordinates into piece coordinates to ensure map has a proper bounding box
tilecenters = merge['tilepx']+numpy.array([merge['mapheader']['xsize']/2,merge['mapheader']['ysize']/2])
tiledist = numpy.sum((tilecenters-c_out)**2,axis=1)
tileidx = numpy.argmin(tiledist)
c_out = c_out - merge['tilepx'][tileidx]
c1 = numpy.fliplr(c1 + c_out)
newnavitem['CoordsInPiece'] = [str(c_out[0]),str(c_out[1]),curr_map['StageXYZ'][2]]
newnavitem['PieceOn'] = [str(merge['sections'][tileidx])]
cnx = numpy.array(numpy.transpose(c1[:,1]))
cnx = numpy.array2string(cnx,separator=' ')
cnx = cnx[2:-2]
cny = numpy.array(numpy.transpose(c1[:,0]))
cny = numpy.array2string(cny,separator=' ')
cny = cny[2:-2]
newnavitem['PtsX'] = cnx.split()
newnavitem['PtsY'] = cny.split()
newnavitem['Note'] = newnavitem['MapFile']
newnavitem['MapID'] = [str(mapid)]
newnavitem['DrawnID'] = curr_map['MapID']
else:
polynav['Type'] = ['1']
polynav['Color'] = ['1']
polynav['NumPts'] = [str(p.shape[0])]
if maps:
newnavitem['Acquire'] = ['1']
else:
newnavitem['Acquire'] = ['0']
newnavitem['MapSection'] = ['0']
newnavitem.pop('SamePosId','')
# newnavitem['MapWidthHeight'] = [str(im2size[0]),str(im2size[1])]
newnavitem['ImageType'] = ['0']
newnavitem['MapMinMaxScale'] = [str(numpy.min(im4)),str(numpy.max(im4))]
newnavitem['NumPts'] = ['5']
newnavitem['# Item'] = 'm_' + label
newnavitem['GroupID'] = [str(newID(nav,startid+50000))]
curr_map['Acquire'] = ['0']
# Polygon
nav_maps.append(newnavitem)
label = mapitem['# Item'] + '_' + str(idx).zfill(3)
#do not export points/polygons when maps are inteded output.
# map corner points
# fill navigator
if not maps:
# Polygon
polynav['# Item'] = label
polynav['Acquire'] = ['1']
polynav['Draw'] = ['1']
polynav['Regis'] = curr_map['Regis']
polynav['Regis'] = mapitem['Regis']
polynav['DrawnID'] = [str(mapid)]
polynav['CoordsInMap'] = [str(int(cx/2)) , str(int(cy/2)),curr_map['StageXYZ'][2]]
polynav['PtsX'] = px.split()
polynav['PtsY'] = py.split()
polynav['GroupID'] = [str(newID(nav,startid+70000))]
polynav['GroupID'] = [str(newID(nav,mapid+70000))]
nav_pol.append(polynav)
def pts2nav(im,pts,cntrs,curr_map,targetitem,nav,sloppy=False,maps=False):
......@@ -1414,7 +1326,7 @@ def pts2nav(im,pts,cntrs,curr_map,targetitem,nav,sloppy=False,maps=False):
# - targetitem, target map
# - nav, all navigator items (emtools dict)
# - sloppy (optional) if merging of original map was sloppy
# - maps (optional) if the virtual maps instead of the points/polygons should be selected for acquisition
# - maps (optional) if the virtual maps instead of the points/polygons should be selected for acquisition
#parse input data
......
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