Closed JLautin closed 8 years ago
Could you attach your FCS file, so I could debug?
Could you also confirm that you're using using python 2.7 rather than python >3?
At the command terminal you can type the following:
python --version
I'm running Python 2.7.10 64-bit on a mac (os x Yosemite).
I've attached a zipped file below, since it didn't support to attach .fcs files. Hope it doesn't mess with your AV too much.
Regards JLautin LMO_bacteria.fcs.zip
Thanks! I will take a look at this over the weekend.
On Thu, Dec 17, 2015 at 9:28 AM, JLautin notifications@github.com wrote:
I'm running Python 2.7.10 64-bit on a mac (os x Yosemite).
I've attached a zipped file below, since it didn't support to attach .fcs files. Hope it doesn't mess with your AV too much.
Regards JLautin LMO_bacteria.fcs.zip https://github.com/eyurtsev/FlowCytometryTools/files/65467/LMO_bacteria.fcs.zip
— Reply to this email directly or view it on GitHub https://github.com/eyurtsev/FlowCytometryTools/issues/9#issuecomment-165465201 .
Eugene Yurtsev
Personal Website: http://eyurtsev.mit.edu
Looks like this is caused by an issue with numpy https://github.com/numpy/numpy/issues/2407
I'll try and release a fix within the next few days
If you need a fix quicker than that you can try and do the following:
1) locate the directory for the fcsparser package
import fcsparser
fcsparser.__path__
2) go to that directory and open api.py
3) Make the following change in the code:
@@ -353,7 +353,8 @@ class FCSParser(object):
# values saved in mixed data formats
dtype = ','.join(par_numeric_type_list)
data = numpy.fromfile(file_handle, dtype=dtype, count=num_events)
- data.dtype.names = self.get_channel_names()
+ names = self.get_channel_names()
+ data.dtype.names = [name.encode('ascii', errors='ignore') for name in names]
else:
# values saved in a single data format
dtype = par_numeric_type_list[0]
where a (-) is remove, and a (+) is add
Fixed in this commit: https://github.com/eyurtsev/fcsparser/commit/398b6b081da599c64ad7b49416bfd921c3a5a061
Please install the newest version of fcsparser (and FlowCytometryTools)
pip install fcsparser==0.1.2
pip install FlowCytometryTools==0.4.5
Thank you for solving it!
/JLautin
Hello!
I have an issue regarding accessing the data segment of my .fcs files with FlowCytometryTools. While accessing the meta data and channels works fine, as soon as I try to access the data, for example through sample.data or transformations I receive the error
"ValueError: item #0 of names is of type unicode and not string"
However, the testfile works just fine. My files are from a Partec Cube 8, in the FCS3.0 format.
Im quite new to the python language, so any help is appreciated.
Regards JLautin