Comments (6)
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
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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
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Thanks! I will take a look at this over the weekend.
On Thu, Dec 17, 2015 at 9:28 AM, JLautin [email protected] 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
#9 (comment)
.
Eugene Yurtsev
Personal Website: http://eyurtsev.mit.edu
from flowcytometrytools.
Looks like this is caused by an issue with numpy numpy/numpy#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:
- locate the directory for the fcsparser package
import fcsparser
fcsparser.__path__
-
go to that directory and open api.py
-
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
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Fixed in this commit: eyurtsev/fcsparser@398b6b0
Please install the newest version of fcsparser (and FlowCytometryTools)
pip install fcsparser==0.1.2
pip install FlowCytometryTools==0.4.5
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Thank you for solving it!
/JLautin
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