def test_read_subblock_meta(data_dir, fname, expected):
with open(data_dir / fname, 'rb') as fp:
czi = CziFile(czi_filename=fp)
data = czi.read_subblock_metadata()
assert expected in data[0][1]
def test_read_unified_subblock_meta(data_dir, fname, expected):
with open(data_dir / fname, 'rb') as fp:
czi = CziFile(czi_filename=fp)
data = czi.read_subblock_metadata(unified_xml=True)
assert expected in etree.tostring(data)
def get_planetable(czifile: str,
norm_time: bool = True,
savetable: bool = False,
separator: str = ',',
index: bool = True) -> Tuple[pd.DataFrame, Optional[str]]:
# get the czi metadata
metadata = czimd.CziMetadata(czifile)
aicsczi = CziFile(czifile)
# initialize the plane table
df_czi = pd.DataFrame(columns=[
'Subblock', 'Scene', 'Tile', 'T', 'Z', 'C', 'X[micron]', 'Y[micron]',
'Z[micron]', 'Time[s]', 'xstart', 'ystart', 'width', 'height'
])
# define subblock counter
sbcount = -1
# check if dimensions are None (because they do not exist for that image)
sizeC = check_dimsize(metadata.image.SizeC, set2value=1)
sizeZ = check_dimsize(metadata.image.SizeZ, set2value=1)
sizeT = check_dimsize(metadata.image.SizeT, set2value=1)
sizeS = check_dimsize(metadata.image.SizeS, set2value=1)
sizeM = check_dimsize(metadata.image.SizeM, set2value=1)
def getsbinfo(subblock: Any) -> Tuple[float, float, float, float]:
try:
# time = sb.xpath('//AcquisitionTime')[0].text
time = subblock.findall(".//AcquisitionTime")[0].text
timestamp = dt.parse(time).timestamp()
except IndexError as e:
timestamp = 0.0
try:
# xpos = np.double(sb.xpath('//StageXPosition')[0].text)
xpos = np.double(subblock.findall(".//StageXPosition")[0].text)
except IndexError as e:
xpos = 0.0
try:
# ypos = np.double(sb.xpath('//StageYPosition')[0].text)
ypos = np.double(subblock.findall(".//StageYPosition")[0].text)
except IndexError as e:
ypos = 0.0
try:
# zpos = np.double(sb.xpath('//FocusPosition')[0].text)
zpos = np.double(subblock.findall(".//FocusPosition")[0].text)
except IndexError as e:
zpos = 0.0
return timestamp, xpos, ypos, zpos
# in case the CZI has the M-Dimension
if metadata.ismosaic:
for s, m, t, z, c in product(range(sizeS), range(sizeM), range(sizeT),
range(sizeZ), range(sizeC)):
sbcount += 1
print("Reading sublock : ", sbcount)
# get x, y, width and height for a specific tile
tilebbox = aicsczi.get_mosaic_tile_bounding_box(S=s,
M=m,
T=t,
Z=z,
C=c)
# read information from subblock
sb = aicsczi.read_subblock_metadata(unified_xml=True,
B=0,
S=s,
M=m,
T=t,
Z=z,
C=c)
# get information from subblock
timestamp, xpos, ypos, zpos = getsbinfo(sb)
df_czi = df_czi.append(
{
'Subblock': sbcount,
'Scene': s,
'Tile': m,
'T': t,
'Z': z,
'C': c,
'X[micron]': xpos,
'Y[micron]': ypos,
'Z[micron]': zpos,
'Time[s]': timestamp,
'xstart': tilebbox.x,
'ystart': tilebbox.y,
'width': tilebbox.w,
'height': tilebbox.h
},
ignore_index=True)
if not metadata.ismosaic:
for s, t, z, c in product(range(sizeS), range(sizeT), range(sizeZ),
range(sizeC)):
sbcount += 1
# get x, y, width and height for a specific tile
tilebbox = aicsczi.get_tile_bounding_box(S=s, T=t, Z=z, C=c)
# read information from subblocks
sb = aicsczi.read_subblock_metadata(unified_xml=True,
B=0,
S=s,
T=t,
Z=z,
C=c)
# get information from subblock
timestamp, xpos, ypos, zpos = getsbinfo(sb)
df_czi = df_czi.append(
{
'Subblock': sbcount,
'Scene': s,
'Tile': 0,
'T': t,
'Z': z,
'C': c,
'X[micron]': xpos,
'Y[micron]': ypos,
'Z[micron]': zpos,
'Time[s]': timestamp,
'xstart': tilebbox.x,
'ystart': tilebbox.y,
'width': tilebbox.w,
'height': tilebbox.h
},
ignore_index=True)
# cast data types
df_czi = df_czi.astype(
{
'Subblock': 'int32',
'Scene': 'int32',
'Tile': 'int32',
'T': 'int32',
'Z': 'int32',
'C': 'int16',
'X[micron]': 'float',
'Y[micron]': 'float',
'Z[micron]': 'float',
'xstart': 'int32',
'ystart': 'int32',
'width': 'int32',
'height': 'int32'
},
copy=False,
errors='ignore')
# normalize time stamps
if norm_time:
df_czi = norm_columns(df_czi, colname='Time[s]', mode='min')
# save planetable as CSV file
if savetable:
csvfile = save_planetable(df_czi,
czifile,
separator=separator,
index=index)
if not savetable:
csvfile = None
return df_czi, csvfile
