def convertFiles(pathToData, outFile, complib='zlib', complevel=9):
seriesName = pathToData.split(os.sep)[-2]
fnl = os.listdir(pathToData)
fnl2 = [pathToData + f for f in fnl]
f1 = read_kdf.ReadKdfData(fnl2[0])
xSize, ySize = f1.shape[0:2]
outF = tables.open_file(outFile, 'w')
filt = tables.Filters(complevel, complib, shuffle=True)
imageData = outF.create_earray(outF.root,
'ImageData',
tables.UInt16Atom(), (0, xSize, ySize),
filters=filt,
expectedrows=len(fnl2))
for fn in fnl2:
imageData.append(read_kdf.ReadKdfData(fn).reshape(1, xSize, ySize))
outF.flush()
outF.close()
def convertFile(pathToData,
outFile,
pixelsize=None,
complib='zlib',
complevel=9):
#seriesName = pathToData.split(os.sep)[-2]
#fnl = os.listdir(pathToData)
#fnl2 = [pathToData + f for f in fnl]
f1 = read_kdf.ReadKdfData(pathToData).squeeze()
xSize, ySize = f1.shape[0:2]
outF = tables.openFile(outFile, 'w')
filt = tables.Filters(complevel, complib, shuffle=True)
imageData = outF.createEArray(outF.root,
'ImageData',
tables.UInt16Atom(), (0, xSize, ySize),
filters=filt,
expectedrows=f1.shape[2])
for i in range(f1.shape[2]):
imageData.append(f1[:, :, i].reshape(1, xSize, ySize))
hdh = MetaData.HDFMDHandler(outF, MetaData.PCODefault)
if not pixelsize == None:
hdh.setEntry('voxelsize.x', pixelsize)
hdh.setEntry('voxelsize.y', pixelsize)
outEvents = outF.createTable(outF.root,
'Events',
SpoolEvent,
filters=tables.Filters(complevel=5,
shuffle=True))
outF.flush()
outF.close()
def OnInit(self):
#wx.InitAllImageHandlers()
print((sys.argv))
bg = None
if (len(sys.argv) > 1):
fnms = os.listdir(sys.argv[1])
else:
raise RuntimeError('Must provide list of files on command line')
if (len(sys.argv) == 3):
bg = read_kdf.ReadKdfData(sys.argv[2])[:, :, :, 0]
fnames = []
for fn in fnms:
fnames.append(sys.argv[1] + fn)
vframe = DSViewFrame(None, filenames=fnames, bg=bg)
self.SetTopWindow(vframe)
vframe.Show(1)
return 1
(options, args) = parser.parse_args()
if options.data is None:
print('Must give a file containing the data')
sys.exit(1)
if options.psf is None:
print('Must give a file containing the psf')
sys.exit(1)
if options.out is None:
print('Must give an output file')
sys.exit(1)
if options.kz is None:
print('Must give the wavelength parameter')
sys.exit(1)
data = squeeze(read_kdf.ReadKdfData(options.data))
psf = squeeze(read_kdf.ReadKdfData(options.psf))
if not options.alpha is None:
alpha = squeeze(read_kdf.ReadKdfData(options.alpha))
else:
alpha = zeros(shape(data), 'f')
print((shape(data)))
print((shape(alpha)))
print((shape(psf)))
servers = []
if not options.servers is None:
svrs = options.servers.split(',')
for s in svrs:
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
##################
from PIL import Image
import read_kdf
import sys
if not (len(sys.argv) == 3):
raise RuntimeError('Usage: kdfToImage infile outfile')
inFile = sys.argv[1]
outFile = sys.argv[2]
im = read_kdf.ReadKdfData(inFile).squeeze()
mode = ''
if (im.dtype.__str__() == 'uint16'):
mode = 'I;16'
elif (im.dtype.__str__() == 'float32'):
mode = 'F'
else:
raise RuntimeError('Error data type <%s> not supported') % im.dtype
Image.fromarray(im, mode).save(outFile)