def query_settings(question, default=1):
"""Ask a question via raw_input() and return an int.
"question" is a string that is presented to the user.
"default" is the presumed answer if the user just hits <Enter>.
It must be an int number (the default) or None (meaning
an answer is required of the user).
The "answer" return value is an int.
"""
cur.execute('SELECT id, name FROM system_setting')
records = cur.fetchall()
ids = []
for record in records:
print str(record[0]) + ' - ' + str(record[1])
ids.append(int(record[0]))
valid = ids
prompt = str(ids)
if not default == None:
prompt = prompt + ' default=' + str(default)
while True:
sys.stdout.write(question + '\n' + prompt + '\n')
choice = raw_input()
if default is not None and choice == '':
if default in valid:
return int(default)
elif int(choice) in valid:
return int(choice)
else:
sys.stdout.write("Please respond with the number of the reqired settings " + str(ids) + "\n")
def initial(name, template=template, init_threshold=0.3, bgfile='image_Ch1.nrrd', alignSet='',
initialSet='--principal-axes'):
cur.execute("SELECT * FROM images_alignment WHERE alignment_stage = 2 AND name like %s", [name])
records = cur.fetchall()
key = []
for desc in cur.description:
key.append(desc[0])
for line in records:
record = dict(zip(key, line))
# clear old failed alignments:
cur.execute("UPDATE images_alignment SET alignment_stage = 2 WHERE last_host = %s AND alignment_stage = 1002",
[str(host)])
cur.connection.commit()
# remove image from stack before processing:
cur.execute("UPDATE images_alignment SET alignment_stage = 1002, last_host = %s WHERE id = %s ",
[str(host), str(record['id'])])
cur.connection.commit()
record = initialRec(record, template, init_threshold, bgfile, alignSet, initialSet)
u = str(record['id']) + ' -> '
for k, v in record.items():
if not (k == 'id' or v == None or v == 'None'):
cur.execute("UPDATE images_alignment SET " + str(k) + "=%s WHERE id = %s ", [v, record['id']])
u = u + str(k) + '=' + str(v) + ', '
print u
cur.connection.commit()
gc.collect()
def warp(name, template=template, bgfile='image_Ch1.nrrd',
warpSet='--grid-spacing 80 --exploration 30 --coarsest 4 --accuracy 0.2 --refine 4 --energy-weight 1e-1'):
cur.execute("SELECT * FROM images_alignment WHERE alignment_stage = 4 AND name like %s", [name])
records = cur.fetchall()
key = []
for desc in cur.description:
key.append(desc[0])
for line in records:
record = dict(zip(key, line))
# clear old failed alignments:
cur.execute("UPDATE images_alignment SET alignment_stage = 4 WHERE last_host = %s AND alignment_stage = 1004",
[str(host)])
cur.connection.commit()
# remove image from stack before processing:
cur.execute("UPDATE images_alignment SET alignment_stage = 1004, last_host = %s WHERE id = %s ",
[str(host), str(record['id'])])
cur.connection.commit()
record = warpRec(record, template, bgfile, warpSet)
u = str(record['id']) + ' -> '
for k, v in record.items():
if not (k == 'id' or v == None or v == 'None'):
cur.execute("UPDATE images_alignment SET " + str(k) + "=%s WHERE id = %s ", [v, record['id']])
u = u + str(k) + '=' + str(v) + ', '
print u
cur.connection.commit()
gc.collect()
def affine(name, template=template, bgfile="image_Ch1.nrrd", affineSet="--dofs 6,9 --auto-multi-levels 4"):
cur.execute("SELECT * FROM images_alignment WHERE alignment_stage = 3 AND name like %s", [name])
records = cur.fetchall()
key = []
for desc in cur.description:
key.append(desc[0])
for line in records:
record = dict(zip(key, line))
# clear old failed alignments:
cur.execute(
"UPDATE images_alignment SET alignment_stage = 3 WHERE last_host = %s AND alignment_stage = 1003",
[str(host)],
)
cur.connection.commit()
# remove image from stack before processing:
cur.execute(
"UPDATE images_alignment SET alignment_stage = 1003, last_host = %s WHERE id = %s ",
[str(host), str(record["id"])],
)
cur.connection.commit()
record = affineRec(record, template, bgfile, affineSet)
u = str(record["id"]) + " -> "
for k, v in record.items():
if not (k == "id" or v == None or v == "None"):
cur.execute("UPDATE images_alignment SET " + str(k) + "=%s WHERE id = %s ", [v, record["id"]])
u = u + str(k) + "=" + str(v) + ", "
print u
cur.connection.commit()
gc.collect()
def merge(name):
cur.execute("SELECT * FROM images_alignment WHERE alignment_stage = 10 AND name like %s", [name])
records = cur.fetchall()
key = []
for desc in cur.description:
key.append(desc[0])
for line in records:
record = dict(zip(key, line))
cur.execute(
"UPDATE images_alignment SET alignment_stage = 1010, last_host = %s WHERE id = %s ",
[str(host), str(record["id"])],
)
cur.connection.commit()
r = mergeRec(record)
u = ""
for k, v in record.items():
if not (k == "id" or v == None or v == "None"):
if not u == "":
u = u + ", "
if type(v) == type(""):
u = u + str(k) + " = '" + str(v) + "'"
else:
u = u + str(k) + " = " + str(v)
print u
cur.execute("UPDATE images_alignment SET " + u + " WHERE id = %s ", [str(record["id"])])
cur.connection.commit()
def convert(name):
cur.execute("SELECT * FROM images_alignment WHERE alignment_stage = 1 AND name like %s", [name])
records = cur.fetchall()
key = []
for desc in cur.description:
key.append(desc[0])
for line in records:
record = dict(zip(key, line))
# remove image from stack before processing:
cur.execute("UPDATE images_alignment SET alignment_stage = 1001, last_host = %s WHERE id = %s ",
[str(host), str(record['id'])])
cur.connection.commit()
r = convRec(record)
u = str(record['id']) + ' -> '
for k, v in record.items():
if not (k == 'id' or v == None or v == 'None'):
cur.execute("UPDATE images_alignment SET " + str(k) + "=%s WHERE id = %s ", [v, record['id']])
u = u + str(k) + '=' + str(v) + ', '
print u
cur.connection.commit()
gc.collect()
)
cur.connection.commit()
r = mergeRec(record)
u = ""
for k, v in record.items():
if not (k == "id" or v == None or v == "None"):
if not u == "":
u = u + ", "
if type(v) == type(""):
u = u + str(k) + " = '" + str(v) + "'"
else:
u = u + str(k) + " = " + str(v)
print u
cur.execute("UPDATE images_alignment SET " + u + " WHERE id = %s ", [str(record["id"])])
cur.connection.commit()
if __name__ == "__main__":
if active and "10" in run_stage:
cur.execute("SELECT name FROM images_alignment WHERE alignment_stage = 10 ORDER BY id")
records = cur.fetchall()
total = len(records)
count = 0
for line in records:
count += 1
print "Converting: " + str(count) + " of " + str(total)
merge(line[0])
print "done"
else:
print "inactive or stage 10 not selected"
[str(host), str(record['id'])])
cur.connection.commit()
record = alignRem(record, template, bgfile, alignSet)
u = str(record['id']) + ' -> '
for k, v in record.items():
if not (k == 'id' or v == None or v == 'None'):
cur.execute("UPDATE images_alignment SET " + str(k) + "=%s WHERE id = %s ", [v, record['id']])
u = u + str(k) + '=' + str(v) + ', '
print u
cur.connection.commit()
gc.collect()
if __name__ == "__main__":
if active and '5' in run_stage:
cur.execute(
"SELECT images_alignment.name, system_template.file, images_original_nrrd.file, system_setting.cmtk_align_var, system_setting.final_pass_level FROM images_alignment, system_template, system_setting, images_original_nrrd WHERE alignment_stage = 5 AND images_original_nrrd.channel = images_alignment.background_channel AND images_original_nrrd.image_id = images_alignment.id AND images_alignment.settings_id = system_setting.id AND system_setting.template_id = system_template.id ORDER BY images_alignment.id")
records = cur.fetchall()
total = len(records)
if total == 0:
cur.execute(
"UPDATE images_alignment SET alignment_stage = 5 FROM (SELECT id FROM images_alignment WHERE alignment_stage = 2005 ORDER BY id LIMIT 2) s WHERE s.id = images_alignment.id")
cur.connection.commit()
gc.collect()
count = 0
print records
for line in records:
count += 1
print 'Warp alignment: ' + str(count) + ' of ' + str(total)
align(line[0], template=(templatedir + line[1]), bgfile=(tempfolder + line[2]), alignSet=line[3],
passLevel=line[4])
print 'done'
import os, sys, nrrd, cmtk, gc, stat, shutil
import numpy as np
import warpScoring.slicescore as slicescore
import warpScoring.CheckImages as ci
from cmtk import cur, tempfolder, active, run_stage, cmtkdir, template, checkDir, host, templatedir
from NRRDtools.labelObjects import labelObj, cutObj, cropObj
if __name__ == "__main__":
if active and '0' in run_stage:
cur.execute("SELECT images_mask_original.id, images_mask_original.intensity_threshold, images_mask_original.min_object_size, images_original_nrrd.file FROM images_mask_original, images_original_nrrd WHERE images_original_nrrd.id = images_mask_original.image_id AND images_mask_original.complete = False ORDER BY images_mask_original.id")
records = cur.fetchall()
total = len(records)
count = 0
print records
for line in records:
count +=1
print 'Create original image mask: ' + str(count) + ' of ' + str(total)
outfile = str(line[3]).replace('.nrrd','-objMask.nrrd').replace('.nrrd', str(line[0]) + '.nrrd')
modfile = str(line[3]).replace('.nrrd','-modFile.nrrd').replace('.nrrd', str(line[0]) + '.nrrd')
if not os.path.isfile(tempfolder + modfile):
shutil.copyfile(tempfolder + str(line[3]), tempfolder + modfile)
objs = labelObj(tempfolder + str(line[3]), tempfolder + outfile, t=line[1], ms=line[2])
cur.execute("UPDATE images_mask_original SET complete=True, cut_complete=False, crop_complete=False, detected_objects=%s WHERE id = %s ", [objs.tolist(), str(line[0])])
cur.connection.commit()
gc.collect()
try:
os.chmod(tempfolder + outfile, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO)
except:
pass
print 'done'
def loadFile(file, folder, settings_id=1, orientation=comp_orien['LPS'], overwrite=False):
r=0
if os.path.exists(file) and ('.tif' in file or '.lsm' in file):
name = str(os.path.splitext(os.path.basename(file))[0])
cur.execute("SELECT count(*) FROM images_alignment WHERE name like %s", [name])
r = int(cur.fetchone()[0])
if r < 1:
cur.execute("INSERT INTO images_alignment (settings_id, name, max_stage, alignment_stage, last_host, loading_host, original_ext, original_path, orig_orientation) VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s)", [str(settings_id), name, str(0), str(1), host, host, str(os.path.splitext(os.path.basename(file))[1]), str(folder), orientation])
cur.connection.commit()
else:
cur.execute("SELECT * FROM images_alignment WHERE name like '" + str(os.path.splitext(os.path.basename(file))[0]) + "'")
print cur.fetchone()
if overwrite:
cur.execute("UPDATE images_alignment SET orig_orientation = %s, settings_id = %s, max_stage = 0, alignment_stage = 1, last_host = %s, loading_host = %s, original_ext = %s, original_path = %s WHERE name = %s", [orientation, str(settings_id), host, host, str(os.path.splitext(os.path.basename(file))[1]), str(folder), name])
cur.connection.commit()
else:
if query_yes_no("Image already exists in processing stack do you want to update original file details?"):
cur.execute("UPDATE images_alignment SET orig_orientation = %s, settings_id = %s, max_stage = 0, alignment_stage = 1, last_host = %s, loading_host = %s, original_ext = %s, original_path = %s WHERE name = %s", [orientation, str(settings_id), host, host, str(os.path.splitext(os.path.basename(file))[1]), str(folder), name])
cur.connection.commit()
cur.execute("SELECT count(*) FROM images_alignment WHERE name like %s", [name])
r = int(cur.fetchone()[0])
gc.collect()
if r > 0:
return True
else:
return False
[str(host), str(record['id'])])
cur.connection.commit()
record = warpRec(record, template, bgfile, warpSet)
u = str(record['id']) + ' -> '
for k, v in record.items():
if not (k == 'id' or v == None or v == 'None'):
cur.execute("UPDATE images_alignment SET " + str(k) + "=%s WHERE id = %s ", [v, record['id']])
u = u + str(k) + '=' + str(v) + ', '
print u
cur.connection.commit()
gc.collect()
if __name__ == "__main__":
if active and '4' in run_stage:
cur.execute(
"SELECT images_alignment.name, system_template.file, images_original_nrrd.file, system_setting.cmtk_warp_var FROM images_alignment, system_template, system_setting, images_original_nrrd WHERE alignment_stage = 4 AND images_original_nrrd.channel = images_alignment.background_channel AND images_original_nrrd.image_id = images_alignment.id AND images_alignment.settings_id = system_setting.id AND system_setting.template_id = system_template.id ORDER BY images_alignment.id")
records = cur.fetchall()
total = len(records)
if total == 0:
cur.execute(
"UPDATE images_alignment SET alignment_stage = 4 FROM (SELECT id FROM images_alignment WHERE alignment_stage = 2004 ORDER BY id LIMIT 2) s WHERE s.id = images_alignment.id")
cur.connection.commit()
gc.collect()
count = 0
print records
for line in records:
count += 1
print 'Warp alignment: ' + str(count) + ' of ' + str(total)
warp(line[0], template=(templatedir + line[1]), bgfile=(tempfolder + line[2]), warpSet=line[3])
# clear old failed alignments:
cur.execute("UPDATE images_alignment SET alignment_stage = 4 WHERE last_host = %s AND alignment_stage = 1004",
def pushLive(id, name, sgfile):
if os.path.exists(sgfile):
if (id > 9999):
first = str(id)[:-4]
last = str(id)[-4:]
else:
first = "000"
last = str(id)
while len(first) < 3:
first = "0" + first
while len(last) < 4:
last = "0" + last
first = "a" + first
if not os.path.exists(tempfolder + "../../IMAGE_DATA/VFB/i/" + first):
os.makedirs(tempfolder + "../../IMAGE_DATA/VFB/i/" + first)
if not os.path.exists(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last):
os.makedirs(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last)
print 'Linking ' + sgfile + ' to ' + tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.nrrd"
if os.path.exists(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.nrrd"):
os.remove(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.nrrd")
shutil.copyfile(sgfile, tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.nrrd")
data, head = nrrd.read(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.nrrd")
if head['sizes'][2] == 185:
print "Inflating from " + str(head['sizes'][2]) + " slices to 270..."
dataNew = np.zeros([head['sizes'][0],head['sizes'][1],270],dtype=np.uint8)
dataNew[:,:,25:210]=data;
head['encoding'] = 'gzip'
if head.has_key('space direction'):
head.pop("space directions", None)
data = dataNew
im = np.transpose(np.max(data,axis=2))
if (data[0][0][0] < 1):
data[0][0][0] = np.uint8(100)
filesize = np.subtract(data.shape, 1)
if (data[filesize[0]][filesize[1]][filesize[2]] < 1):
data[filesize[0]][filesize[1]][filesize[2]] = np.uint8(100)
nrrd.write(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.nrrd", data, options=head)
print "Creating Thumbnail"
im = Image.fromarray(im)
if np.shape(im)[0] < np.shape(im)[1]:
im = im.resize((120,60), Image.ANTIALIAS)
elif np.shape(im)[0] > np.shape(im)[1]:
im = im.resize((60,120), Image.ANTIALIAS)
else:
im = im.resize((60,60), Image.ANTIALIAS)
im.save(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/thumbnail.png","PNG")
print "Converting to Tiff"
subprocess.call(Fiji + " -macro nrrd2tif.ijm " + tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.nrrd" + " -batch", shell=True)
if os.path.isfile(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.wlz"):
os.remove(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.wlz")
print "Clearing old woolz data..."
print "Creating wlz: " + "/VFB/i/" + first + "/" + last + "/volume.wlz"
print "Using voxel sizes: Z:" + str(head['space directions'][2][2]) + ", X:" + str(head['space directions'][0][0]) + ", Y:" + str(head['space directions'][1][1])
subprocess.call("nice " + wlzDir + "WlzExtFFConvert -f tif -F wlz " + tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.tif |" + wlzDir + "WlzThreshold -v50 |" + wlzDir + "WlzSetVoxelSize -z" + str(head['space directions'][2][2]) + " -x" + str(head['space directions'][0][0]) + " -y" + str(head['space directions'][1][1]) + " >" + tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.wlz" , shell=True)
cur.execute("UPDATE images_alignment SET alignment_stage = 21, notes = %s WHERE id = %s", [str("VFB_"+first+last),str(id)])
cur.connection.commit()
print "Clearing up..."
os.remove(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.tif")
else:
print "Skipping " + name
gc.collect()
if os.path.isfile(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.wlz"):
os.remove(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.wlz")
print "Clearing old woolz data..."
print "Creating wlz: " + "/VFB/i/" + first + "/" + last + "/volume.wlz"
print "Using voxel sizes: Z:" + str(head['space directions'][2][2]) + ", X:" + str(head['space directions'][0][0]) + ", Y:" + str(head['space directions'][1][1])
subprocess.call("nice " + wlzDir + "WlzExtFFConvert -f tif -F wlz " + tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.tif |" + wlzDir + "WlzThreshold -v50 |" + wlzDir + "WlzSetVoxelSize -z" + str(head['space directions'][2][2]) + " -x" + str(head['space directions'][0][0]) + " -y" + str(head['space directions'][1][1]) + " >" + tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.wlz" , shell=True)
cur.execute("UPDATE images_alignment SET alignment_stage = 21, notes = %s WHERE id = %s", [str("VFB_"+first+last),str(id)])
cur.connection.commit()
print "Clearing up..."
os.remove(tempfolder + "../../IMAGE_DATA/VFB/i/" + first + "/" + last + "/volume.tif")
else:
print "Skipping " + name
gc.collect()
if __name__ == "__main__":
if active and '5' in run_stage:
cur.execute("SELECT id, name, aligned_sg FROM images_alignment WHERE alignment_stage = 11 ORDER BY images_alignment.id")
records = cur.fetchall()
for line in records:
try:
pushLive(line[0], line[1], sgfile=(tempfolder + line[2]))
except:
cur.execute("UPDATE images_alignment SET alignment_stage = 21, notes = 'FAILED' WHERE id = %s", [str(line[0])])
cur.connection.commit()
print 'done'
else:
print 'inactive or stage 4 not selected'
def convRec(record):
try:
if not 'loading_host' in record:
record['loading_host'] = 'roberts-mbp'
if not record['loading_host'] == host:
print 'Warning: ' + host + ' is not the loading host (' + record['loading_host'] + ')'
if str(record['original_path']).endswith(os.path.sep):
file = record['original_path'] + record['name'] + record['original_ext']
else:
file = record['original_path'] + os.path.sep + record['name'] + record['original_ext']
print 'Converting ' + file
if (os.path.exists(file) or os.path.exists(file + '.gz')):
record['last_host'] = host
if (os.path.exists(file + '.gz') and (not os.path.exists(file))):
check_call(['gzip', '-d', file + '.gz'])
if '.gz' in file:
check_call(['gzip', '-df', file])
file = str(file).replace('.gz', '')
if str(record['original_ext']) == '.gz':
record['name'] = str(os.path.splitext(os.path.basename(file))[0])
record['original_ext'] = str(os.path.splitext(os.path.basename(file))[1])
print 'Opening file: ' + file + '...'
tif = TiffFile(file)
image = tif.asarray()
print 'Converting file: ' + file + '...'
record = checkDir(record)
if tif.is_lsm:
metadata = tif[0].cz_lsm_scan_information
voxelZ = metadata['plane_spacing']
voxelY = metadata['line_spacing']
voxelX = metadata['sample_spacing']
header = {}
header['encoding'] = 'gzip'
header['space directions'] = [[float(voxelX), 0.0, 0.0], [0.0, float(voxelY), 0.0],
[0.0, 0.0, float(voxelZ)]]
header['space units'] = ['"microns"', '"microns"', '"microns"']
# header['keyvaluepairs'] = dict(metadata)
# print header
else:
metadata = tif[0].image_description
# metadata = json.loads(metadata.decode('utf-8'))
# voxel = metadata['Voxel size']
# TBD: resolve zoxel size!
voxelZ = 0.5
voxelY = 0.5
voxelX = 0.5
#temp fix for zebrafish:
if (record['settings_id'] == 10):
voxelZ = 1
voxelY = 1
voxelX = 1
header = {}
header['encoding'] = 'gzip'
header['space directions'] = [[float(voxelX), 0.0, 0.0], [0.0, float(voxelY), 0.0],
[0.0, 0.0, float(voxelZ)]]
header['space units'] = ['"px"', '"px"', '"px"']
print(image.shape, image.dtype)
if image.ndim > 4:
sh = np.array(image.shape)
rmdim = np.argmin(sh)
if sh[rmdim] > 1:
sh[rmdim] = np.max(sh)
rmdim = np.argmin(sh)
image = np.max(image, axis=rmdim)
print 'slimmed down to:'
print(image.shape, image.dtype)
print metadata
# TBD: add voxel size data
# header['keyvaluepairs'] = dict(metadata)
tif.close()
check_call(['gzip', '-f', file])
image = np.squeeze(image)
sh = np.array(np.shape(image))
ch = np.argmin(sh)
iy = np.argmax(sh)
sh[iy] = 0
ix = np.argmax(sh)
sh[ix] = 0
iz = np.argmax(sh)
sh = np.shape(image)
# move channel to last axis:
image = np.swapaxes(image, ch, -1)
# move smalest (Z) axis to last axis before channel:
image = np.swapaxes(image, iz, -2)
# swap X & Y to match NRRD standard order for saving:
image = np.swapaxes(image, 0, 1)
print record['name'] + record['original_ext'] + ' - ' + str(np.shape(image))
rt = 0
mt = 0
sg = 0
bg = 0
cur.execute(
"SELECT system_template.orientation FROM system_template, system_setting, images_alignment WHERE images_alignment.id = %s AND images_alignment.settings_id = system_setting.id AND system_setting.template_id = system_template.id",
[record['id']])
tempOrien = cur.fetchone()[0]
cur.execute(
"SELECT system_setting.auto_balance_th FROM system_template, system_setting, images_alignment WHERE images_alignment.id = %s AND images_alignment.settings_id = system_setting.id AND system_setting.template_id = system_template.id",
[record['id']])
tempTresh = float(cur.fetchone()[0])
if 'orig_orientation' not in record.keys():
if sh[ch] == 2:
record['orig_orientation'] = comp_orien[tempOrien]
else:
record['orig_orientation'] = 'right-posterior-inferior' # needs to be set at load
if record['orig_orientation'] == '':
if sh[ch] == 2:
record['orig_orientation'] = comp_orien[tempOrien]
else:
record['orig_orientation'] = 'right-posterior-inferior' # needs to be set at load
header['space'] = comp_orien[tempOrien]
for c in xrange(0, sh[ch]):
upd = {}
chan, Nbound, hist = ab.AutoBalance(np.squeeze(image[:, :, :, c]), threshold=tempTresh, background=0)
print 'Ch' + str(c + 1) + ' - ' + str(np.shape(chan))
Sname = tempfolder + record['name'] + '_Ch' + str(c + 1) + '.nrrd'
if not record['orig_orientation'] == comp_orien[tempOrien]:
chan = ro.reorientate(np.uint8(chan), curOr=record['orig_orientation'],
targOr=comp_orien[tempOrien])
else:
chan = np.uint8(chan)
if not ((record['crop_xyz'] is None) or (record['crop_xyz'] is '')):
cut = map(int, str(record['crop_xyz']).replace('[', '').replace(']', '').split(','))
cut = np.array(cut)
if np.sum(cut) > 0:
print 'cropping: (' + str(cut) + ')...'
sh = np.shape(chan)
print sh
chan = chan[cut[0]:sh[0] - cut[1], cut[2]:sh[1] - cut[3], cut[4]:sh[2] - cut[5]]
print np.shape(chan)
print 'saving...'
nrrd.write(Sname, chan, options=header)
upd.update(
{'image_id': record['id'], 'channel': + int(c + 1), 'file': str(Sname).replace(tempfolder, ''),
'pre_histogram': list(hist), 'new_min': int(Nbound['min']), 'new_max': int(Nbound['max'])})
print str(upd)
cur.execute(
"SELECT count(*) FROM images_original_nrrd WHERE image_id = %(image_id)s AND channel = %(channel)s",
upd)
r = cur.fetchone()[0]
if r > 0:
cur.execute(
"UPDATE images_original_nrrd SET file = %(file)s, pre_hist = %(pre_histogram)s, new_min = %(new_min)s, new_max = %(new_max)s, is_index = False WHERE image_id = %(image_id)s AND channel = %(channel)s",
upd)
cur.connection.commit()
else:
cur.execute(
"INSERT INTO images_original_nrrd (image_id, channel, file, pre_hist, new_min, new_max, is_index) VALUES (%(image_id)s, %(channel)s, %(file)s, %(pre_histogram)s, %(new_min)s, %(new_max)s, False)",
upd)
cur.connection.commit()
try:
os.chmod(Sname, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO)
except:
pass
ct = sum(chan[chan > 20])
if ct > rt:
rt = ct
bg = c + 1
if mt == 0:
mt = ct
sg = c + 1
if ct < mt:
mt = ct
sg = c + 1
print 'BG: ' + str(bg) + ', SG: ' + str(sg)
if record['background_channel'] == 0:
record['background_channel'] = bg
if record['signal_channel'] == 0:
record['signal_channel'] = sg
record['alignment_stage'] = 2
# record.update({'original_nrrd': upd})
record['max_stage'] = 2
# collection.save(record)
print 'conversion complete.'
del upd, hist, chan, Nbound, tif, image, sh, ch, iy, ix, iz, Sname, rt, bg, ct, mt, sg
else:
record['alignment_stage'] = 1001
if record['notes'] is None:
record['notes'] = time.strftime(
"%c") + ' Error finding file ' + file + ' on ' + host
else:
record['notes'] = record['notes'] + '\n' + time.strftime(
"%c") + ' Error finding file ' + file + ' on ' + host
except Exception, e:
print str(e)
record['alignment_stage'] = 0
if record['notes'] is None:
record['notes'] = time.strftime(
"%c") + ' Error with handling uploaded file by ' + host
else:
record['notes'] = record['notes'] + '\n' + time.strftime(
"%c") + ' Error with handling uploaded file by ' + host
[str(host), str(record['id'])])
cur.connection.commit()
r = convRec(record)
u = str(record['id']) + ' -> '
for k, v in record.items():
if not (k == 'id' or v == None or v == 'None'):
cur.execute("UPDATE images_alignment SET " + str(k) + "=%s WHERE id = %s ", [v, record['id']])
u = u + str(k) + '=' + str(v) + ', '
print u
cur.connection.commit()
gc.collect()
if __name__ == "__main__":
if active and '1' in run_stage:
cur.execute("SELECT name FROM images_alignment WHERE alignment_stage = 1 ORDER BY id")
records = cur.fetchall()
total = len(records)
if total == 0:
# add any paused records to the active list
cur.execute(
"UPDATE images_alignment SET alignment_stage = 1 FROM (SELECT id FROM images_alignment WHERE alignment_stage = 2001 ORDER BY id LIMIT 2) s WHERE s.id = images_alignment.id")
# clear old failed alignments:
cur.execute(
"UPDATE images_alignment SET alignment_stage = 1 WHERE last_host = %s AND alignment_stage = 1001",
[str(host)])
cur.connection.commit()
gc.collect()
count = 0
for line in records:
count += 1