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Although there's a lot of subjects related to my question already, the answers are usually no understandable for me, as I am just a beginner in the "writting scripts in Python" field.
Here is my situation :
There's a machine learning software that writes models in a .pkl format at the end of its learning phase. I would like to make those model.pkl files openable by an operator to check what there is inside the model. Thus I began to write a script that would use the pickle.load method and write the data contained in my model.pkl into a .txt file. Here's what I wrote to begin with:
import pickle
import os
model_path=input("Model Path = ")
with open(model_path, "rb") as model :
load = pickle.load(model, encoding='utf-8')
new_model_path = model_path.split('.pkl')[0] +'.txt'
print("creating new file at : ", new_model_path)
model_readable = open(new_model_path, 'rt')
model_readable.write(load)
print("writing model as readable : ", load)
model_readable.close()
model.close()
If I try to run it here's the output :
python3.7 unpickler.py
Model Path = /home/ouriacc/Desktop/workspace/SESAM/Base_de_tests/Anomalie_1/Models/OCSVM/EyeSat/CI_HEATER_CAMERA_VOLTAGE.pkl
Traceback (most recent call last):
File "unpickler.py", line 7, in <module>
load = pickle.load(model, encoding='utf-8')
_pickle.UnpicklingError: invalid load key, '_'.
I couldn't find any explanation about this error that didn't imply an incomplete or corrupted download, which can't be my case here as the model.pkl files are not modified once they've been created by the AI software.
Could someone help me to solve the error or even indicate me an other methode to achieve my goal ? All I need is a script that gives access for a user to what the .pkl file contains.
Thank you very much !
So I figured out why #wundermahn asked about scikit-learn. It seems my model.pkl files were generated by joblib and not exactly pickle library. This is why it wouldn't work apparently. It changed my code by replacing pickle.load() by joblid.load() and it works better !
Thank you !
I'm attempting to read in a series of files for processing contained in a single directory using RedVox:
input_directory = "/home/ben/Documents/Data/F1D1/21" # file location
rdvx_data = DataWindow(input_dir=input_directory, apply_correction=False, debug=True) # using RedVox to read in the files
print(os.listdir(input_directory)) # verifying the files actually exist...
# returns "['file1.rdvxz', 'file2.rdvxz', file3.rdvxz', ...etc]", they exist
# write audio portion to file
rdvx_data.to_json_file(base_dir=output_rpd_directory,
file_name=output_filename)
# this never runs, because rdvx_data.stations = [] (verified through debugging)
for station in rdvx_data.stations:
# some code here
Enabling debugging through arguments as seen above does not provide an extra details. In fact, there is no error message whatsoever. It writes the JSON file and pickle to disk, but the JSON file is full of null values and the pickle object is just a shell, no contents. So the files definitely exist, os.listdir() sees them, but RedVox does not.
I assume this is some very silly error or lack of understanding on my part. Any help is greatly appreciated. I have not worked with RedVox previously, nor do I have much understanding of what these files contain other than some audio data and some other data. I've simply been tasked with opening them to work on a model to analyze the data within.
SOLVED: Not sure why the previous code doesn't work (it was handed to me), however, I worked around the DataWindow call and went straight to calling the "redvox.api900.reader" object:
from redvox.api900 import reader
dataset_dir = "/home/*****/Documents/Data/F1D1/21/"
rdvx_files = glob(dataset_dir+"*.rdvxz")
for file in rdvx_files:
wrapped_packet = reader.read_rdvxz_file(file)
From here I can view all of the sensor data within:
if wrapped_packet.has_microphone_sensor():
microphone_sensor = wrapped_packet.microphone_sensor()
print("sample_rate_hz", microphone_sensor.sample_rate_hz())
Hope this helps anyone else who's confused.
I'm on a Debian GNU/Linux computer, working with Python 2.7.9.
As a part of my job, I have been making python scripts that read inputs in various formats (e.g. Excel, Csv, Txt) and parse the information to more standarized files. It's not my first time opening or working with Excel files.
There's a particular file which is giving me problems, I just can't open it. When I tried with xlrd (version 0.9.3), it gave me the following error:
xlrd.open_workbook('sample.xls')
XLRDError: Unsupported format, or corrupt file: BOF not
workbook/worksheet: op=0x0009 vers=0x0002 strm=0x000a build=0 year=0
-> BIFF21
I tried to investigate the matter on my own, found a couple of answers in StackOverflow but I couldn't open it anyway. This particular answer I found may be the problem (the second explanation), but it doesn't include a workaround: https://stackoverflow.com/a/16518707/4345659
A tool that could conert the file to csv/txt would also solve the problem.
I already tried with:
xlrd
openpyxl
xlsx2csv (the shell tool)
A sample file is available here:
https://ufile.io/r4m6j
As a side note, I can open it with LibreOffice Calc and MS Excel, so I could eventually change it to csv that way. The thing is, I need to do it all with a python script.
Thanks in advance!
It seems like MS Problem. The xls file is very strange, maybe you should contact xlrd support.
But I have a crazy workaround for you: xls2ods. It works for me even though xls2csv doesn't (SiC!).
So, install catdoc first:
$sudo apt-get install catdoc
Then convert your xls file to ods and open ods using pyexcel_ods or whatever you prefer. To use pyexcel_ods install it first using pip install pyexcel_ods.
import subprocess
from pyexcel_ods import get_data
file_basename = 'sample'
returncode = subprocess.call(['xls2ods', '{}.xls'.format(file_basename)])
if returnecode > 0:
# consider to use subprocess.Popen if you need more control on stderr
exit(returncode)
data = get_data('{}.ods'.format(file_basename))
print(data)
I'm getting following output:
OrderedDict([(u'sample',
[[u'labo',
u'codfarm',
u'farmacia',
u'direccion',
u'localidad',
u'nom_medico',
u'matricula',
u'troquel',
u'producto',
u'cant_total']])])
Here is a kludge I would use:
Assuming you have LibreOffice on Debian, you could either convert all your *.xls files into *.csv using:
import os
os.system("libreoffice --headless --convert-to csv *.xls")
#or use os.call
... and then work consistently with csv.
Or you could convert only the corrupted file(s) when needed using a try/except block:
import os
try:
xlrd.open_workbook('sample.xls')
except XLRDError:
os.system("libreoffice --headless --convert-to csv sample.xls")
# mycsv = open("sample.csv", "r")
# for line in mycsv.readlines():
# ...
# ...
OBS: Keep LibreOffice closed while running the script.
Alternatively there are other tools out there to do the conversion. Here is one (which I have not tested): https://github.com/dilshod/xlsx2csv
If you are targeting windows, if you have Excel installed, and if you are familiar with Excel VBA, you will have a quick solution using the comtypes package:
http://pythonhosted.org/comtypes/
You will have direct access to Excel by its COM interfaces.
This code open an xls file and saves it as a cvs file, using the comtypes package:
import comtypes.client as cl
progId = "Excel.Application.15"
xl = cl.CreateObject(progId)
wb = xl.Workbooks.Open(r"C:\Users\aUser\Desktop\thermoList.xls")
wb.SaveAs(r"C:\Users\aUser\Desktop\thermoList.csv",FileFormat=6)
xl.DisplayAlerts = False
xl.Quit()
I could not test it with "sample.xls" which is corrupt.
Your could try with another file.
You might need to adjust the progId according to your version of Excel.
It's a file format issue. I'm not sure what file type is it but it's not Excel. I just open and saved the file with sample2.xls name and compare the types:
How are you creating this file?
If you need to get the words as a list of strings:
text_file = open("sample.xls", "r")
lines = text_file.read().replace(chr(200), '').replace(chr(0), '').replace(chr(1), '').replace(chr(5), '').replace(chr(2), '').replace(chr(3), '').replace(chr(4), '').replace(chr(6), '').replace(chr(7), '').replace(chr(8), '').replace(chr(9), '').replace(chr(10), '').replace(chr(12), '').replace(chr(15), '').replace(chr(16), '').replace(chr(17), '').replace(chr(18), '').replace(chr(49), '').replace('Arial', '')
for line in lines.split(chr(128)):
print(line)
the output:
The file you provided is corrupted, so there is no way for other responders to test it and recommend a good solution. And exception you posted confirming that.
As a solution you can try to debug some things, please see some steps below:
You mentioned you tried the xlrd library. Try to check if your xlrd module is upto date by executing this:
Python 2.7.9
>>> import xlrd
>>> xlrd.__VERSION
update to the latest official version if needed
Try to open any other *.xls file and see if it works with Python version you're using and current library.
Check module documentation it's pretty good, and there are some different things described how to use this module on various platforms( Win vs. Linux)http://xlrd.readthedocs.io/en/latest/dates.html
You always can rich out to the community (there is still a chance that you might be getting into some weird state or bug) the link is here https://github.com/python-excel/xlrd/issues
Hope that helps.
Unable to open your Excel either. Just as yadayada said, I think it is the problem of data source. If you really want to figure out the reason, I suggest you ask questions about the excel instead of python.
It's always work for me with any xls or xlsx files:
def csv_from_excel(filename_xls, filename_csv):
wb = xlrd.open_workbook(filename_xls, encoding_override='YOUR_ENCODING_HERE (f.e. "cp1251"')
sh = wb.sheet_by_index(0)
your_csv_file = open(filename_csv, 'wb')
wr = unicodecsv.writer(your_csv_file)
for rownum in xrange(sh.nrows):
wr.writerow(sh.row_values(rownum))
your_csv_file.close()
So, i don't work directly with excel file before convert them to csv. Mb it will help you
for working with MS word files in python, there is python win32 extensions, which can be used in windows. How do I do the same in linux?
Is there any library?
Use the native Python docx module. Here's how to extract all the text from a doc:
document = docx.Document(filename)
docText = '\n\n'.join(
paragraph.text for paragraph in document.paragraphs
)
print(docText)
See Python DocX site
Also check out Textract which pulls out tables etc.
Parsing XML with regexs invokes cthulu. Don't do it!
You could make a subprocess call to antiword. Antiword is a linux commandline utility for dumping text out of a word doc. Works pretty well for simple documents (obviously it loses formatting). It's available through apt, and probably as RPM, or you could compile it yourself.
benjamin's answer is a pretty good one. I have just consolidated...
import zipfile, re
docx = zipfile.ZipFile('/path/to/file/mydocument.docx')
content = docx.read('word/document.xml').decode('utf-8')
cleaned = re.sub('<(.|\n)*?>','',content)
print(cleaned)
OpenOffice.org can be scripted with Python: see here.
Since OOo can load most MS Word files flawlessly, I'd say that's your best bet.
I know this is an old question, but I was recently trying to find a way to extract text from MS word files, and the best solution by far I found was with wvLib:
http://wvware.sourceforge.net/
After installing the library, using it in Python is pretty easy:
import commands
exe = 'wvText ' + word_file + ' ' + output_txt_file
out = commands.getoutput(exe)
exe = 'cat ' + output_txt_file
out = commands.getoutput(exe)
And that's it. Pretty much, what we're doing is using the commands.getouput function to run a couple of shell scripts, namely wvText (which extracts text from a Word document, and cat to read the file output). After that, the entire text from the Word document will be in the out variable, ready to use.
Hopefully this will help anyone having similar issues in the future.
Take a look at how the doc format works and create word document using PHP in linux. The former is especially useful. Abiword is my recommended tool. There are limitations though:
However, if the document has complicated tables, text boxes, embedded spreadsheets, and so forth, then it might not work as expected. Developing good MS Word filters is a very difficult process, so please bear with us as we work on getting Word documents to open correctly. If you have a Word document which fails to load, please open a Bug and include the document so we can improve the importer.
(Note: I posted this on this question as well, but it seems relevant here, so please excuse the repost.)
Now, this is pretty ugly and pretty hacky, but it seems to work for me for basic text extraction. Obviously to use this in a Qt program you'd have to spawn a process for it etc, but the command line I've hacked together is:
unzip -p file.docx | grep '<w:t' | sed 's/<[^<]*>//g' | grep -v '^[[:space:]]*$'
So that's:
unzip -p file.docx: -p == "unzip to stdout"
grep '<w:t': Grab just the lines containing '<w:t' (<w:t> is the Word 2007 XML element for "text", as far as I can tell)
sed 's/<[^<]>//g'*: Remove everything inside tags
grep -v '^[[:space:]]$'*: Remove blank lines
There is likely a more efficient way to do this, but it seems to work for me on the few docs I've tested it with.
As far as I'm aware, unzip, grep and sed all have ports for Windows and any of the Unixes, so it should be reasonably cross-platform. Despit being a bit of an ugly hack ;)
If your intention is to use purely python modules without calling a subprocess, you can use the zipfile python modude.
content = ""
# Load DocX into zipfile
docx = zipfile.ZipFile('/home/whateverdocument.docx')
# Unpack zipfile
unpacked = docx.infolist()
# Find the /word/document.xml file in the package and assign it to variable
for item in unpacked:
if item.orig_filename == 'word/document.xml':
content = docx.read(item.orig_filename)
else:
pass
Your content string however needs to be cleaned up, one way of doing this is:
# Clean the content string from xml tags for better search
fullyclean = []
halfclean = content.split('<')
for item in halfclean:
if '>' in item:
bad_good = item.split('>')
if bad_good[-1] != '':
fullyclean.append(bad_good[-1])
else:
pass
else:
pass
# Assemble a new string with all pure content
content = " ".join(fullyclean)
But there is surely a more elegant way to clean up the string, probably using the re module.
Hope this helps.
Unoconv might also be a good alternative: http://linux.die.net/man/1/unoconv
To read Word 2007 and later files, including .docx files, you can use the python-docx package:
from docx import Document
document = Document('existing-document-file.docx')
document.save('new-file-name.docx')
To read .doc files from Word 2003 and earlier, make a subprocess call to antiword. You need to install antiword first:
sudo apt-get install antiword
Then just call it from your python script:
import os
input_word_file = "input_file.doc"
output_text_file = "output_file.txt"
os.system('antiword %s > %s' % (input_word_file, output_text_file))
If you have LibreOffice installed, you can simply call it from the command line to convert the file to text, then load the text into Python.
Is this an old question?
I believe that such thing does not exist.
There are only answered and unanswered ones.
This one is pretty unanswered, or half answered if you wish.
Well, methods for reading *.docx (MS Word 2007 and later) documents without using COM interop are all covered.
But methods for extracting text from *.doc (MS Word 97-2000), using Python only, lacks.
Is this complicated?
To do: not really, to understand: well, that's another thing.
When I didn't find any finished code, I read some format specifications and dug out some proposed algorithms in other languages.
MS Word (*.doc) file is an OLE2 compound file.
Not to bother you with a lot of unnecessary details, think of it as a file-system stored in a file. It actually uses FAT structure, so the definition holds. (Hm, maybe you can loop-mount it in Linux???)
In this way, you can store more files within a file, like pictures etc.
The same is done in *.docx by using ZIP archive instead.
There are packages available on PyPI that can read OLE files. Like (olefile, compoundfiles, ...)
I used compoundfiles package to open *.doc file.
However, in MS Word 97-2000, internal subfiles are not XML or HTML, but binary files.
And as this is not enough, each contains an information about other one, so you have to read at least two of them and unravel stored info accordingly.
To understand fully, read the PDF document from which I took the algorithm.
Code below is very hastily composed and tested on small number of files.
As far as I can see, it works as intended.
Sometimes some gibberish appears at the start, and almost always at the end of text.
And there can be some odd characters in-between as well.
Those of you who just wish to search for text will be happy.
Still, I urge anyone who can help to improve this code to do so.
doc2text module:
"""
This is Python implementation of C# algorithm proposed in:
http://b2xtranslator.sourceforge.net/howtos/How_to_retrieve_text_from_a_binary_doc_file.pdf
Python implementation author is Dalen Bernaca.
Code needs refining and probably bug fixing!
As I am not a C# expert I would like some code rechecks by one.
Parts of which I am uncertain are:
* Did the author of original algorithm used uint32 and int32 when unpacking correctly?
I copied each occurence as in original algo.
* Is the FIB length for MS Word 97 1472 bytes as in MS Word 2000, and would it make any difference if it is not?
* Did I interpret each C# command correctly?
I think I did!
"""
from compoundfiles import CompoundFileReader, CompoundFileError
from struct import unpack
__all__ = ["doc2text"]
def doc2text (path):
text = u""
cr = CompoundFileReader(path)
# Load WordDocument stream:
try:
f = cr.open("WordDocument")
doc = f.read()
f.close()
except: cr.close(); raise CompoundFileError, "The file is corrupted or it is not a Word document at all."
# Extract file information block and piece table stream informations from it:
fib = doc[:1472]
fcClx = unpack("L", fib[0x01a2l:0x01a6l])[0]
lcbClx = unpack("L", fib[0x01a6l:0x01a6+4l])[0]
tableFlag = unpack("L", fib[0x000al:0x000al+4l])[0] & 0x0200l == 0x0200l
tableName = ("0Table", "1Table")[tableFlag]
# Load piece table stream:
try:
f = cr.open(tableName)
table = f.read()
f.close()
except: cr.close(); raise CompoundFileError, "The file is corrupt. '%s' piece table stream is missing." % tableName
cr.close()
# Find piece table inside a table stream:
clx = table[fcClx:fcClx+lcbClx]
pos = 0
pieceTable = ""
lcbPieceTable = 0
while True:
if clx[pos]=="\x02":
# This is piece table, we store it:
lcbPieceTable = unpack("l", clx[pos+1:pos+5])[0]
pieceTable = clx[pos+5:pos+5+lcbPieceTable]
break
elif clx[pos]=="\x01":
# This is beggining of some other substructure, we skip it:
pos = pos+1+1+ord(clx[pos+1])
else: break
if not pieceTable: raise CompoundFileError, "The file is corrupt. Cannot locate a piece table."
# Read info from pieceTable, about each piece and extract it from WordDocument stream:
pieceCount = (lcbPieceTable-4)/12
for x in xrange(pieceCount):
cpStart = unpack("l", pieceTable[x*4:x*4+4])[0]
cpEnd = unpack("l", pieceTable[(x+1)*4:(x+1)*4+4])[0]
ofsetDescriptor = ((pieceCount+1)*4)+(x*8)
pieceDescriptor = pieceTable[ofsetDescriptor:ofsetDescriptor+8]
fcValue = unpack("L", pieceDescriptor[2:6])[0]
isANSII = (fcValue & 0x40000000) == 0x40000000
fc = fcValue & 0xbfffffff
cb = cpEnd-cpStart
enc = ("utf-16", "cp1252")[isANSII]
cb = (cb*2, cb)[isANSII]
text += doc[fc:fc+cb].decode(enc, "ignore")
return "\n".join(text.splitlines())
I'm not sure if you're going to have much luck without using COM. The .doc format is ridiculously complex, and is often called a "memory dump" of Word at the time of saving!
At Swati, that's in HTML, which is fine and dandy, but most word documents aren't so nice!
Just an option for reading 'doc' files without using COM: miette. Should work on any platform.
Aspose.Words Cloud SDK for Python is a platform independent solution to convert MS Word/Open Office files to text. It is a commercial product but free trial plan provides 150 monthly API calls.
P.S: I am a developer evangelist at Aspose.
# For complete examples and data files, please go to https://github.com/aspose-words-cloud/aspose-words-cloud-python
# Import module
import asposewordscloud
import asposewordscloud.models.requests
from shutil import copyfile
# Please get your Client ID and Secret from https://dashboard.aspose.cloud.
client_id='xxxxxxx-xxxx-xxxx-xxxxx-xxxxxxxxxx'
client_secret='xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx'
words_api = asposewordscloud.WordsApi(client_id,client_secret)
words_api.api_client.configuration.host='https://api.aspose.cloud'
filename = 'C:/Temp/02_pages.docx'
dest_name = 'C:/Temp/02_pages.txt'
#Convert RTF to text
request = asposewordscloud.models.requests.ConvertDocumentRequest(document=open(filename, 'rb'), format='txt')
result = words_api.convert_document(request)
copyfile(result, dest_name)
I'm hoping my problem can be solved with some geojson expertise. The problem I'm having has to do with RhinoPython - the embedded IronPython engine in McNeel's Rhino 5 (more info here: http://python.rhino3d.com/). I don't think its necessary to be an expert on RhinoPython to answer this question.
I'm trying to load a geojson file in RhinoPython. Because you can't import the geojson module into RhinoPython like in Python I'm using this custom module GeoJson2Rhino provided here: https://github.com/localcode/rhinopythonscripts/blob/master/GeoJson2Rhino.py
Right now my script looks like this:
`import rhinoscriptsyntax as rs
import sys
rp_scripts = "rhinopythonscripts"
sys.path.append(rp_scripts)
import rhinopythonscripts
import GeoJson2Rhino as geojson
layer_1 = rs.GetLayer(layer='Layer 01')
layer_color = rs.LayerColor(layer_1)
f = open('test_3.geojson')
gj_data = geojson.load(f,layer_1,layer_color)
f.close()`
In particular:
f = open('test_3.geojson')
gj_data = geojson.load(f)
works fine when I'm trying to extract geojson data from regular python 2.7. However in RhinoPython I'm getting the following error message: Message: expected string for parameter 'text' but got 'file'; in reference to gj_data = geojson.load(f).
I've been looking at the GeoJson2Rhino script linked above and I think I've set the parameters for the function correctly. As far as I can tell it doesn't seem to recognize my geojson file, and wants it as a string. Is there an alternative file open function I can use to get the function to recognize it as a geojson file?
Judging by the error message, it looks like the load method requires a string as the first input but in the above example a file object is being passed instead. Try this...
f = open('test_3.geojson')
g = f.read(); # read contents of 'f' into a string
gj_data = geojson.load(g)
...or, if you don't actually need the file object...
g = open('test_3.geojson').read() # get the contents of the geojson file directly
gj_data = geojson.load(g)
See here for more information about reading files in python.