I trying to read dicom file with python3 and pydicom library. For some dicom data, I can't get data correctly and get error messages when I tried to print the result of pydicom.dcmread.
However, I have tried to use python2 and it worked well. I checked out the meta information and compared it with other dicom files which can be processed, I didn't find any difference between them.
import pydiom
ds = pydicom.dcmread("xxxxx.dicom")
print(ds)
Traceback (most recent call last):
File "generate_train_data.py", line 387, in <module>
tf.app.run()
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/platform/app.py", line 125, in run
_sys.exit(main(argv))
File "generate_train_data.py", line 371, in main
create_ann()
File "generate_train_data.py", line 368, in create_ann
ds_ann_dir, case_name, merge_channel=False)
File "generate_train_data.py", line 290, in process_dcm_set
all_dcms, dcm_truth_infos = convert_dicoms(dcm_list, zs)
File "generate_train_data.py", line 179, in convert_dicoms
instance_num, pixel_spacing, img_np = extract_info(dcm_path)
File "generate_train_data.py", line 147, in extract_info
print(ds)
UnicodeEncodeError: 'ascii' codec can't encode characters in position 2277-2279: ordinal not in range(128)
Anyone has come across the same problem?
Can you give an example for such a dicom file? When running the pydicom example with python 3.7 it's working perfectly:
import matplotlib.pyplot as plt
import pydicom
from pydicom.data import get_testdata_files
filename = get_testdata_files("CT_small.dcm")[0]
ds = pydicom.dcmread(filename)
plt.imshow(ds.pixel_array, cmap=plt.cm.bone)
It's also working with the sample dicom files from the Medical Image Samples.
I believe the cause of the problem is that Python (for me it only happened in Python 3 running on Centos 7.6 Linux printing to a terminal window on MacOS) is not able to figure out how to print a string that contains a non-ascii character because of the setting of the locale. You can use the locale command to see the results. Mine started out with everything set to "C". I set the LANG environment variable to en_US.UTF-8. With that setting it worked for me.
In csh this is done using
setenv LANG en_US.UTF-8
In bash use:
export LANG=en_US.UTF-8
My problem resulted from having 'ยต' in the Series Description element. The file was an attenuation map from a SPECT reconstruction on a Siemens scanner. I used the following Python code to help figure out the problem.
#! /usr/bin/env python3
import pydicom as dicom
from sys import exit, argv
def myprint(ds, indent=0):
"""Go through all items in the dataset and print them with custom format
Modelled after Dataset._pretty_str()
"""
dont_print = ['Pixel Data', 'File Meta Information Version']
indent_string = " " * indent
next_indent_string = " " * (indent + 1)
for data_element in ds:
if data_element.VR == "SQ": # a sequence
print(indent_string, data_element.name)
for sequence_item in data_element.value:
myprint(sequence_item, indent + 1)
print(next_indent_string + "---------")
else:
if data_element.name in dont_print:
print("""<item not printed -- in the "don't print" list>""")
else:
repr_value = repr(data_element.value)
if len(repr_value) > 50:
repr_value = repr_value[:50] + "..."
try:
print("{0:s} {1:s} = {2:s}".format(indent_string,
data_element.name,
repr_value))
except:
print(data_element.name,'****Error printing value')
for f in argv[1:]:
ds = dicom.dcmread(f)
myprint(ds, indent=1)
This is based on the myprint function from]1
The code tries to print out all the data items. It catches exceptions and prints "****Error printing value" when there is an error.
Related
I recently re-activated a python project from last year. It still worked. I recently bought a new computer and upgraded to Windows 11. I also updated my Pycharm to the latest and updated to python 10.1. The program no longer works. Which update is the culprit?
Below shows the essence of the code which does not work. I can successfully download .jpg files but not .pdf files.
from wand.image import Image
file1 = 'U:/Image Files/Bonnie Dundee.jpg'
print(file1)
img1 = Image(filename=file1, resolution=300)
file2 = 'U:/Image Files/Frosty Morning.pdf'
print(file2)
img2 = Image(filename=file2, resolution=300)
The error trace is:
C:\Users\jradc\PycharmProjects\Scratch\venv\Scripts\python.exe C:/Users/jradc/PycharmProjects/Scratch/main.py
U:/Image Files/Bonnie Dundee.jpg
U:/Image Files/Frosty Morning.pdf
Traceback (most recent call last):
File "C:\Users\jradc\PycharmProjects\Scratch\main.py", line 7, in <module>
img2 = Image(filename=file2, resolution=300)
File "C:\Users\jradc\PycharmProjects\Scratch\venv\lib\site-packages\wand\image.py", line 9144, in __init__
self.read(filename=filename)
File "C:\Users\jradc\PycharmProjects\Scratch\venv\lib\site-packages\wand\image.py", line 9815, in read
self.raise_exception()
File "C:\Users\jradc\PycharmProjects\Scratch\venv\lib\site-packages\wand\resource.py", line 222, in raise_exception
raise e
wand.exceptions.DelegateError: FailedToExecuteCommand `"gswin64c.exe" -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 "-sDEVICE=pngalpha" -dTextAlphaBits=4 -dGraphicsAlphaBits=4 "-r300x300" -dPrinted=false "-sOutputFile=C:/Users/jradc/AppData/Local/Temp/magick-xx4FiylIV-id96p7igp2OZkQb3jLaJ_t%d" "-fC:/Users/jradc/AppData/Local/Temp/magick-wcsbcSOqVJ1dFFk0CAU_gvAVIYrZi1Ut" "-fC:/Users/jradc/AppData/Local/Temp/magick-1GWjBArMZle6Xrv-HTjtyKzCqE1Csf8H"' (The system cannot find the file specified.
) # error/delegate.c/ExternalDelegateCommand/516
Process finished with exit code 1
Could anyone point to what I need to change to get this back to working?
I corrected the file extension.
Looks like the system could not find gswin64c.exe.
py-Wand uses that to convert PDF to PNG.
Check that ghostscript (you probably want the AGPL release) is installed and in your Path.
In the "explorer", search for gswin64c.exe and note the directory where it is.
Then look for "Environment variables" in the start menu and verify that the aforementioned directory is in the Path. If not, edit the path and add it.
I have just installed ocropus OCR with all dependencies in my windows 7 machine. (I am using 32bit python 2.7) It seems to be working fine except that I cannot load the default OCR model: en-default.pyrnn.gz. , and receiving a Traceback. I am using the following syntax:
python ocropus-rpred -m en-default.pyrnn.gz book\0001\*.png
here is the error
INFO: #inputs47
# loading object /usr/local/share/ocropus/en-default.pyrnn.gz
Traceback (most recent call last):
File "ocropus-rpred" line 109, in <module>
network = ocrolib.load_object(args.model,verbose=1)
File "C:\anaconda32\lib\site-packages\ocrolib\common.py", line 513, in load_object
return unpickler.load()
EOFError
I have checked the file is not empty; also double checked the binary mode flag enabled i.e. "wb" and "rb"; also converted the newlines of common.py using dos2unix. I am being unable to unable to solve this problem. If anyone have expereinced similar issues, kindly share.
import cPickle
import gzip
def save_object(fname,obj,zip=0):
if zip==0 and fname.endswith(".gz"):
zip = 1
if zip>0:
# with gzip.GzipFile(fname,"wb") as stream:
with os.popen("gzip -9 > '%s'"%fname,"wb") as stream:
cPickle.dump(obj,stream,2)
else:
with open(fname,"wb") as stream:
cPickle.dump(obj,stream,2)
def unpickle_find_global(mname,cname):
if mname=="lstm.lstm":
return getattr(lstm,cname)
if not mname in sys.modules.keys():
exec "import "+mname
return getattr(sys.modules[mname],cname)
def load_object(fname,zip=0,nofind=0,verbose=0):
"""Loads an object from disk. By default, this handles zipped files
and searches in the usual places for OCRopus. It also handles some
class names that have changed."""
if not nofind:
fname = ocropus_find_file(fname)
if verbose:
print "# loading object",fname
if zip==0 and fname.endswith(".gz"):
zip = 1
if zip>0:
# with gzip.GzipFile(fname,"rb") as stream:
with os.popen("gunzip < '%s'"%fname,"rb") as stream:
unpickler = cPickle.Unpickler(stream)
unpickler.find_global = unpickle_find_global
return unpickler.load()
else:
with open(fname,"rb") as stream:
unpickler = cPickle.Unpickler(stream)
unpickler.find_global = unpickle_find_global
return unpickler.load()
UPDATE: Hi, please note that I have used Python's native gzip, and it is working fine. Thank you for pointing that out. Here is the correct syntax that is working on Windows: {with gzip.GzipFile(fname,"rb") as stream:}
Your use of gunzip (in the load_object function) is incorrect. Unless passed the -c argument, gunzip writes the decompressed data to a new file, not to its stdout (which is what you seem to be attempting to do).
As a result, it doesn't write anything to its stdout, and your stream variable contains no data, hence the EOFError.
A quick fix is to change your gunzip command line to give it the -c argument.
More info here: http://linux.die.net/man/1/gzip
That said, why are you even shelling out to gunzip to decompress your data? Python's built-in gzip module should handle that without problems.
I am trying to run a python file from the command line with a single parameter in Ubuntu 12.04. The program works if I simply run it from the IDE and pass the parameter in the code. However, if I call 'python readFromSerial1.py 3' in the command prompt, I get:
Traceback (most recent call last):
File "readFromSerial1.py", line 62, in <module>
main()
File "readFromSerial1.py", line 6, in main
readDataFromUSB(time)
File "readFromSerial1.py", line 9, in readDataFromUSB
import usb.core
ImportError: No module named usb.core
I'm a little confused as the module imports correctly if I run from the IDE. I download the pyUSB module and extracted it (its filename is pyusb-1.0.0a3). I then copied this file into
/usr/local/lib/python2.7/site-packages/. Is that the correct procedure? I have a feeling the issue is due to python simply not being able to find the usb module and I need to put it in the correct location. My code is below, and any help would be greatly appreciated:
readFromSerial1.py
import sys
def main():
time = sys.argv[1]
#time = 1
readDataFromUSB(time)
def readDataFromUSB(time):
import usb.core
#find device
dev = usb.core.find(idVendor=0x099e, idProduct=0x0001) #GPS info
#Was the device found?
if dev is None:
raise ValueError('Device not found')
else:
print "Device found!"
#Do this to avoid 'Errno16: Resource is busy'
if dev.is_kernel_driver_active(0):
try:
dev.detach_kernel_driver(0)
except usb.core.USBError as e:
sys.exit("Could not detach kernel driver: %s" % str(e))
#Sets default config
dev.set_configuration()
#Gets default endpoint
endpoint = dev[0][(0,0)][0]
writeObject = open("InputData.txt", "w")
#iterate for time purposes
for i in range(0, (time*6)): #sys.argv is command line variable for time input
data = dev.read(endpoint.bEndpointAddress, endpoint.wMaxPacketSize, 0, 100000)
sret = ''.join([chr(x) for x in data])
writeObject.write(sret);
print sret
'''
newStr = ''.join(sret[7:14])
compareStr = ",*4F"
if (newStr == compareStr):
print "The GPS is not reading in any values right now. Try going somewhere else with better reception."
else:
print sret[7:14]
'''
writeObject.close()
main()
I haven't figure out how to do pickle load/save's between python 2 and 3 with pandas DataFrames. There is a 'protocol' option in the pickler that I've played with unsuccessfully but I'm hoping someone has a quick idea for me to try. Here is the code to get the error:
python2.7
>>> import pandas; from pylab import *
>>> a = pandas.DataFrame(randn(10,10))
>>> a.save('a2')
>>> a = pandas.DataFrame.load('a2')
>>> a = pandas.DataFrame.load('a3')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/site-packages/pandas-0.10.1-py2.7-linux-x86_64.egg/pandas/core/generic.py", line 30, in load
return com.load(path)
File "/usr/local/lib/python2.7/site-packages/pandas-0.10.1-py2.7-linux-x86_64.egg/pandas/core/common.py", line 1107, in load
return pickle.load(f)
ValueError: unsupported pickle protocol: 3
python3
>>> import pandas; from pylab import *
>>> a = pandas.DataFrame(randn(10,10))
>>> a.save('a3')
>>> a = pandas.DataFrame.load('a3')
>>> a = pandas.DataFrame.load('a2')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.3/site-packages/pandas-0.10.1-py3.3-linux-x86_64.egg/pandas/core/generic.py", line 30, in load
return com.load(path)
File "/usr/local/lib/python3.3/site-packages/pandas-0.10.1-py3.3-linux-x86_64.egg/pandas/core/common.py", line 1107, in load
return pickle.load(f)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xf4 in position 0: ordinal not in range(128)
Maybe expecting pickle to work between python version is a bit optimistic?
I had the same problem. You can change the protocol of the dataframe pickle file with the following function in python3:
import pickle
def change_pickle_protocol(filepath,protocol=2):
with open(filepath,'rb') as f:
obj = pickle.load(f)
with open(filepath,'wb') as f:
pickle.dump(obj,f,protocol=protocol)
Then you should be able to open it in python2 no problem.
If somebody uses pandas.DataFrame.to_pickle() then do the following modification in source code to have the capability of pickle protocol setting:
1) In source file /pandas/io/pickle.py (before modification copy the original file as /pandas/io/pickle.py.ori) search for the following lines:
def to_pickle(obj, path):
pkl.dump(obj, f, protocol=pkl.HIGHEST_PROTOCOL)
Change these lines to:
def to_pickle(obj, path, protocol=pkl.HIGHEST_PROTOCOL):
pkl.dump(obj, f, protocol=protocol)
2) In source file /pandas/core/generic.py (before modification copy the original file as /pandas/core/generic.py.ori) search for the following lines:
def to_pickle(self, path):
return to_pickle(self, path)
Change these lines to:
def to_pickle(self, path, protocol=None):
return to_pickle(self, path, protocol)
3) Restart your python kernel if it runs then save your dataframe using any available pickle protocol (0, 1, 2, 3, 4):
# Python 2.x can read this
df.to_pickle('my_dataframe.pck', protocol=2)
# protocol will be the highest (4), Python 2.x can not read this
df.to_pickle('my_dataframe.pck')
4) After pandas upgrade, repeat step 1 & 2.
5) (optional) Ask the developers to have this capability in official releases (because your code will throw exception on any other Python environments without these changes)
Nice day!
You can override the highest protocol available for the pickle package:
import pickle as pkl
import pandas as pd
if __name__ == '__main__':
# this constant is defined in pickle.py in the pickle package:"
pkl.HIGHEST_PROTOCOL = 2
# 'foo.pkl' was saved in pickle protocol 4
df = pd.read_pickle(r"C:\temp\foo.pkl")
# 'foo_protocol_2' will be saved in pickle protocol 2
# and can be read in pandas with Python 2
df.to_pickle(r"C:\temp\foo_protocol_2.pkl")
This is definitely not an elegant solution but it does the work without changing pandas code directly.
UPDATE: I found that the newer version of pandas, allow to specify the pickle version in the .to_pickle function:
https://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.to_pickle.html[1]
DataFrame.to_pickle(path, compression='infer', protocol=4)
I keep getting the following error:
$ ./test.py
-bash: ./test.py: cannot execute binary file
when trying to run the following file in python via cygwin:
#!usr/bin/python
with open("input.txt") as inf:
try:
while True:
latin = inf.next().strip()
gloss = inf.next().strip()
trans = inf.next().strip()
process(latin, gloss, trans)
inf.next() # skip blank line
except StopIteration:
# reached end of file
pass
from itertools import chain
def chunk(s):
"""Split a string on whitespace or hyphens"""
return chain(*(c.split("-") for c in s.split()))
def process(latin, gloss, trans):
chunks = zip(chunk(latin), chunk(gloss))
How do I fix this??
After taking on the below suggestions, still getting the same error.
If this helps, I tried
$ python ./test.py
and got
$ python ./test.py
File "./test.py", line 1
SyntaxError: Non-ASCII character '\xff' in file ./test.py on line 1, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details
There is a problem. You are missing the '/' in front of usr in #!usr/bin/python. Your line should look like this.
#!/usr/bin/python
In addition to protecting the file executable, #!/usr/bin/python may not work. At least it has never worked for me on Red Hat or Ubuntu Linux. Instead, I have put this in my Python files:
#!/usr/bin/env python
I don't know how this works on Windows platforms.