jstitlow
commented
5 years ago Sorry, this was a file format issue caused by loss of metadata during image pre-processing.
Closed jstitlow closed 5 years ago
jstitlow
commented
5 years ago Sorry, this was a file format issue caused by loss of metadata during image pre-processing.
Any ideas?
(chromagnon) bioc1301@mprocessor1:~/data/20190710_CaMKIIYFP_YFP647ATTO_MB112c_myrSNAP_JF546SNAP_viol/image$ chromagnon 100719_CaMKIIYFP_YFP647ATTO_MB112c_myrSNAP_JF546SNAP_viol_1h_p1l_heel.tif -R ../cal/100719_CaMKIIYFP_YFP647ATTO_MB112c_myrSNAP_JF546SNAP_viol_1h_p1l_heel.tif -E dv
couldn't load module(s): P /usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/Chromagnon/imgio/bioformatsIO.py:92: UserWarning: Traceback (most recent call last): File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/Chromagnon/imgio/bioformatsIO.py", line 23, in
import bioformats # reading bioformats is necessary to know if JDK is required or not (in init)
File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/bioformats/init.py", line 19, in
import javabridge
File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/javabridge/init.py", line 38, in
from .jutil import start_vm, kill_vm, vm, activate_awt, deactivate_awt
File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/javabridge/jutil.py", line 155, in
import javabridge._javabridge as _javabridge
ImportError: libjvm.so: cannot open shared object file: No such file or directory
warnings.warn(errs, UserWarning) Traceback (most recent call last): File "/usr/people/bioc1301/miniconda3/envs/chromagnon/bin/chromagnon", line 11, in
load_entry_point('Chromagnon==0.81', 'console_scripts', 'chromagnon')()
File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/Chromagnon/chromagnon.py", line 642, in command_line
h = imgio.Reader(fn)
File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/Chromagnon/imgio/init.py", line 35, in Reader
return _switch(fn, read=True, *args, *kwds)
File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/Chromagnon/imgio/init.py", line 98, in _switch
return klasses['tif'](fn, args, **kwds)
File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/Chromagnon/imgio/multitifIO.py", line 29, in init
generalIO.GeneralReader.init(self, fn)
File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/Chromagnon/imgio/generalIO.py", line 41, in init
self.openFile()
File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/Chromagnon/imgio/multitifIO.py", line 38, in openFile
self.readHeader()
File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/Chromagnon/imgio/multitifIO.py", line 41, in readHeader
self.readMetaData()
File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/Chromagnon/imgio/multitifIO.py", line 184, in readMetaData
pz = _convertUnit(pz, unit)
File "/usr/people/bioc1301/miniconda3/envs/chromagnon/lib/python2.7/site-packages/Chromagnon/imgio/multitifIO.py", line 21, in _convertUnit
factor = factors[fromwhat] - factors[towhat] or 0
KeyError: 'pixel'