Error while running code

[sanh642]

ModuleNotFoundError Traceback (most recent call last)

in 4 import random 5 from shutil import copyfile ----> 6 import pydicom as dicom 7 import cv2 ModuleNotFoundError: No module named 'pydicom' When i Import Pydicom and when install pydicom my anaconda just search but dont install 

[lindawangg]

I installed using pip install pydicom. You can also install using these instructions since you're using anaconda: https://anaconda.org/conda-forge/pydicom.

[sanh642]

Thanks for ur reply but if I run it through pip whats the procedure then as with conda im unable to run this code in jupytor

[SHREYAS1188]

Hello @sanh642 Try installing using conda prompt it will work

[sanh642]

Thanks

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On Fri, Jun 5, 2020 at 12:24 PM Shreyas . Potdar notifications@github.com wrote:

Hello @sanh642 https://github.com/sanh642 Try installing using conda prompt it will work

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-639306966, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQXWNUERQSBNRBUKU73RVCMTHANCNFSM4NPIANKQ .

-- Thanks Sania

[sanh642]

[image: image.png]

Im unable to install opencv kindly help how can I install it with conda command prompt. Kindly tell me the correct command

Thanks Sania

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On Fri, Jun 5, 2020 at 7:08 PM Sania Hafeez saniahafeez1990@gmail.com wrote:

Thanks

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On Fri, Jun 5, 2020 at 12:24 PM Shreyas . Potdar notifications@github.com wrote:

Hello @sanh642 https://github.com/sanh642 Try installing using conda prompt it will work

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-639306966, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQXWNUERQSBNRBUKU73RVCMTHANCNFSM4NPIANKQ .

-- Thanks Sania

-- Thanks Sania

[josephius]

I usually install opencv with pip using the command:

pip install opencv-python

[SHREYAS1188]

@sanh642 Having already installed anaconda navigator

1. start
2. search conda prompt [ it opens like terminal interface ]
3. enter command : pip install opencv-python if already installed it gives you the version of installation or installs by itself.

this should work fine if any query do ask.

[sanh642]

heye Hope u r doing well kindly guide me for running your COVID-

On Wed, Jun 10, 2020 at 7:40 PM Shreyas . Potdar notifications@github.com wrote:

@sanh642 https://github.com/sanh642 if u have not installed anaconda then install it first using https://www.anaconda.com/products/individual#:~:text=Anaconda%20Navigator%20is%20a%20desktop,without%20using%20command%2Dline%20commands .

once installed

1. start
2. search conda prompt [ it opens like terminal interface ]
3. enter command : pip install opencv-python if already installed it gives you the version of installation or installs by itself.

this should work fine if any query do ask.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-642054339, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQTKTIWBUIMWBKCZGXLRV6LN5ANCNFSM4NPIANKQ .

-- Thanks Sania

[sanh642]

Hye Hope You are doing well

Kindly guide me to run project COVID - Net on github I am running that code but needs guidance plz help me as soon as possible

Thanks Sania

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On Wed, Jun 10, 2020 at 7:40 PM Shreyas . Potdar notifications@github.com wrote:

@sanh642 https://github.com/sanh642 if u have not installed anaconda then install it first using https://www.anaconda.com/products/individual#:~:text=Anaconda%20Navigator%20is%20a%20desktop,without%20using%20command%2Dline%20commands .

once installed

1. start
2. search conda prompt [ it opens like terminal interface ]
3. enter command : pip install opencv-python if already installed it gives you the version of installation or installs by itself.

this should work fine if any query do ask.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-642054339, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQTKTIWBUIMWBKCZGXLRV6LN5ANCNFSM4NPIANKQ .

-- Thanks Sania

[sanh642]

Hye May I know plz dat how to run the code dat you provided on github regarding Covid-Net. Like which file to run first and which model you ised Thank Sania

On 10 Jun 2020 8:02 p.m., "Sania Hafeez" saniahafeez1990@gmail.com wrote:

Hye Hope You are doing well

Kindly guide me to run project COVID - Net on github I am running that code but needs guidance plz help me as soon as possible

Thanks Sania

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On Wed, Jun 10, 2020 at 7:40 PM Shreyas . Potdar notifications@github.com wrote:

@sanh642 https://github.com/sanh642 if u have not installed anaconda then install it first using https://www.anaconda.com/products/individual#:~:text= Anaconda%20Navigator%20is%20a%20desktop,without%20using% 20command%2Dline%20commands.

once installed

1. start
2. search conda prompt [ it opens like terminal interface ]
3. enter command : pip install opencv-python if already installed it gives you the version of installation or installs by itself.

this should work fine if any query do ask.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-642054339, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQTKTIWBUIMWBKCZGXLRV6LN5ANCNFSM4NPIANKQ .

-- Thanks Sania

[sanh642]

[image: image.png]

Why Im getting this error Kindly guide me how can I crete dataset As I have uploaded all the date related to this project the same way u provided instructions.

Kindly help me as I am very confused that from where I start my work

Thanks Sania

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On Thu, Jun 11, 2020 at 8:23 PM Sania Hafeez saniahafeez1990@gmail.com wrote:

Hye May I know plz dat how to run the code dat you provided on github regarding Covid-Net. Like which file to run first and which model you ised Thank Sania

On 10 Jun 2020 8:02 p.m., "Sania Hafeez" saniahafeez1990@gmail.com wrote:

Hye Hope You are doing well

Kindly guide me to run project COVID - Net on github I am running that code but needs guidance plz help me as soon as possible

Thanks Sania

https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon Virus-free. www.avast.com https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link <#m_2032604671213638191m-5894920207694757854_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Wed, Jun 10, 2020 at 7:40 PM Shreyas . Potdar < notifications@github.com> wrote:

@sanh642 https://github.com/sanh642 if u have not installed anaconda then install it first using https://www.anaconda.com/products/individual#:~:text=Anaconda%20Navigator%20is%20a%20desktop,without%20using%20command%2Dline%20commands .

once installed

1. start
2. search conda prompt [ it opens like terminal interface ]
3. enter command : pip install opencv-python if already installed it gives you the version of installation or installs by itself.

this should work fine if any query do ask.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-642054339, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQTKTIWBUIMWBKCZGXLRV6LN5ANCNFSM4NPIANKQ .

-- Thanks Sania

-- Thanks Sania

[SHREYAS1188]

hey! Actually what i see here is that many models have been developed as and when they have received the data like for example create_COVIDx_V2.ipynb which is the main file to build your model the images required for training and testing the name of those images you will get it in respective textfiles like test_COVIDx2.txt and i guess you will have to run first data.py then go to create_COVIDx_V2.ipynb and then eval.py . Even i am a newbie here so if something wrong please help me correct.
i hope the methods i told will work fine:)

[sanh642]

Thanks will try if face any other problem then will let u know

On Fri, Jun 12, 2020 at 8:03 AM Shreyas . Potdar notifications@github.com wrote:

hey! Actually what i see here is that many models have been developed as and when they have received the data like for example create_COVIDx_V2.ipynb which is the main file to build your model the images required for training and testing the name of those images you will get it in respective textfiles like test_COVIDx2.txt and i guess you will have to run first data.py then go to create_COVIDx_V2.ipynb and then eval.py . Even i am a newbie here so if something wrong please help me correct. i hope the methods i told will work fine:)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-643038310, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQR5EZ2NUU6UDSEX6C3RWGLGJANCNFSM4NPIANKQ .

-- Thanks Sania

[sanh642]

I am unable to run files with .py extension in jupyter notebook can u help me thanks

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On Fri, Jun 12, 2020 at 10:35 PM Sania Hafeez saniahafeez1990@gmail.com wrote:

Thanks will try if face any other problem then will let u know

On Fri, Jun 12, 2020 at 8:03 AM Shreyas . Potdar notifications@github.com wrote:

hey! Actually what i see here is that many models have been developed as and when they have received the data like for example create_COVIDx_V2.ipynb which is the main file to build your model the images required for training and testing the name of those images you will get it in respective textfiles like test_COVIDx2.txt and i guess you will have to run first data.py then go to create_COVIDx_V2.ipynb and then eval.py . Even i am a newbie here so if something wrong please help me correct. i hope the methods i told will work fine:)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-643038310, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQR5EZ2NUU6UDSEX6C3RWGLGJANCNFSM4NPIANKQ .

-- Thanks Sania

-- Thanks Sania

[SHREYAS1188]

to run files in juypter notebook you should have .ipynb file extension

[sanh642]

in your project Covid net on github there are some files with .py extension how will I run those ??

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On Sat, Jun 13, 2020 at 11:46 AM Shreyas . Potdar notifications@github.com wrote:

to run files in juypter notebook you should have .ipynb file extension

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-643580191, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQVS2SVLP7RK5GKXRALRWMOEBANCNFSM4NPIANKQ .

-- Thanks Sania

[sanh642]

[image: image.png] [image: image.png] [image: image.png] [image: image.png] [image: image.png]

Why i am getting these errors and how will i solve these issues kindly help where to get these missing files Thanks Sania

On Sat, Jun 13, 2020 at 11:36 PM Sania Hafeez saniahafeez1990@gmail.com wrote:

in your project Covid net on github there are some files with .py extension how will I run those ??

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On Sat, Jun 13, 2020 at 11:46 AM Shreyas . Potdar < notifications@github.com> wrote:

to run files in juypter notebook you should have .ipynb file extension

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-643580191, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQVS2SVLP7RK5GKXRALRWMOEBANCNFSM4NPIANKQ .

-- Thanks Sania

-- Thanks Sania

[CHANANEHassen]

I'm getting this error someone could help plz ?

File "C:\Users\chana\anaconda3\envs\tensorflow\lib\shutil.py", line 121, in copyfile with open(dst, 'wb') as fdst:

FileNotFoundError: [Errno 2] No such file or directory: 'data\train\SARS-10.1148rg.242035193-g04mr34g0-Fig8c-day10.jpeg'

[jgmontoya]

@CHANANEHassen Did you create the data directory (with both train and test directories inside)?

[CHANANEHassen]

@CHANANEHassen Did you create the data directory (with both train and test directories inside)?

[CHANANEHassen]

@jgmontoya No i haven't. i just run the code How and where should I create the data directory?

[jgmontoya]

In the root of the repo, so next to to the following directories which already exist:

• annotations
• assets
• docs
• .github

just create the following ones:

• data
  • test
  • train

(test and train should be inside data)

Also remember that you have to download the datasets (as explained here)

[CHANANEHassen]

@jgmontoya thank you so much for clearing things out

[SHREYAS1188]

[image: image.png] [image: image.png] [image: image.png] [image: image.png] [image: image.png] Why i am getting these errors and how will i solve these issues kindly help where to get these missing files Thanks Sania On Sat, Jun 13, 2020 at 11:36 PM Sania Hafeez saniahafeez1990@gmail.com wrote: … in your project Covid net on github there are some files with .py extension how will I run those ?? https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon Virus-free. www.avast.com https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link <#m_-8025828685967641842_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Sat, Jun 13, 2020 at 11:46 AM Shreyas . Potdar < @.***> wrote: > to run files in juypter notebook you should have .ipynb file extension > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#74 (comment)>, > or unsubscribe > https://github.com/notifications/unsubscribe-auth/APZGFQVS2SVLP7RK5GKXRALRWMOEBANCNFSM4NPIANKQ > . > -- Thanks Sania -- Thanks Sania

i was a bit late but i cant see the images of error

[sanh642]

[image: image.png]4

Kindly check dis and guide me first plz and some files are missing too

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On Wed, Jun 17, 2020 at 11:26 AM Shreyas . Potdar notifications@github.com wrote:

[image: image.png] [image: image.png] [image: image.png] [image: image.png] [image: image.png] Why i am getting these errors and how will i solve these issues kindly help where to get these missing files Thanks Sania On Sat, Jun 13, 2020 at 11:36 PM Sania Hafeez saniahafeez1990@gmail.com wrote: … <#m1298663892886891511> in your project Covid net on github there are some files with .py extension how will I run those ?? https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon Virus-free. www.avast.com https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link <#m_-8025828685967641842_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Sat, Jun 13, 2020 at 11:46 AM Shreyas . Potdar < @.***> wrote: > to run files in juypter notebook you should have .ipynb file extension > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#74 (comment) https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-643580191>,

or unsubscribe > https://github.com/notifications/unsubscribe-auth/APZGFQVS2SVLP7RK5GKXRALRWMOEBANCNFSM4NPIANKQ . > -- Thanks Sania -- Thanks Sania

i was a bit late but i cant see the images of error

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-645178201, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQWWS5KH3LIAYAGPZADRXBO2BANCNFSM4NPIANKQ .

-- Thanks Sania

[sanh642]

file not found error kindly let me know how can i get these files

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On Wed, Jun 17, 2020 at 11:26 PM Sania Hafeez saniahafeez1990@gmail.com wrote:

[image: image.png]4

Kindly check dis and guide me first plz and some files are missing too

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On Wed, Jun 17, 2020 at 11:26 AM Shreyas . Potdar < notifications@github.com> wrote:

[image: image.png] [image: image.png] [image: image.png] [image: image.png] [image: image.png] Why i am getting these errors and how will i solve these issues kindly help where to get these missing files Thanks Sania On Sat, Jun 13, 2020 at 11:36 PM Sania Hafeez saniahafeez1990@gmail.com wrote: … <#m_-4251913034537936988_m1298663892886891511> in your project Covid net on github there are some files with .py extension how will I run those ?? https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon Virus-free. www.avast.com https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link <#m_-8025828685967641842_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Sat, Jun 13, 2020 at 11:46 AM Shreyas . Potdar < @.***> wrote: > to run files in juypter notebook you should have .ipynb file extension > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#74 (comment) https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-643580191>,

or unsubscribe > https://github.com/notifications/unsubscribe-auth/APZGFQVS2SVLP7RK5GKXRALRWMOEBANCNFSM4NPIANKQ . > -- Thanks Sania -- Thanks Sania

i was a bit late but i cant see the images of error

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-645178201, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQWWS5KH3LIAYAGPZADRXBO2BANCNFSM4NPIANKQ .

-- Thanks Sania

-- Thanks Sania

[jgmontoya]

We can't see the images you're sending, I think using the web interface instead of replying via email should work

[sanh642]

okay let me try it again or copy error here

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On Thu, Jun 18, 2020 at 12:57 AM Javier G. Montoya S. < notifications@github.com> wrote:

We can't see the images you're sending, I think using the web interface instead of replying via email should work

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-645591111, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQUZDPFF5OOTKKBHNHDRXEN4HANCNFSM4NPIANKQ .

-- Thanks Sania

[sanh642]

FileNotFoundError Traceback (most recent call last) in 1 # adapted from https://github.com/mlmed/torchxrayvision/blob/master/torchxrayvision/datasets.py#L814----> 2 cohen_csv = pd.read_csv(cohen_csvpath, nrows=None) 3 #idx_pa = csv["view"] == "PA" # Keep only the PA view 4 views = ["PA", "AP", "AP Supine", "AP semi erect", "AP erect"] 5 cohen_idx_keep = cohen_csv.view.isin(views) ~\anaconda3\lib\site-packages\pandas\io\parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision) 674 ) 675 --> 676 return _read(filepath_or_buffer, kwds) 677 678 parser_f.name = name ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _read(filepath_or_buffer, kwds) 446 447 # Create the parser.--> 448 parser = TextFileReader(fp_or_buf, kwds) 449 450 if chunksize or iterator: ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, f, engine, kwds) 878 self.options["has_index_names"] = kwds["has_index_names"] 879 --> 880 self._make_engine(self.engine) 881 882 def close(self): ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _make_engine(self, engine) 1112 def _make_engine(self, engine="c"): 1113 if engine == "c":-> 1114 self._engine = CParserWrapper(self.f, self.options) 1115 else: 1116 if engine == "python": ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, src, kwds) 1889 kwds["usecols"] = self.usecols 1890 -> 1891 self._reader = parsers.TextReader(src, **kwds) 1892 self.unnamed_cols = self._reader.unnamed_cols 1893 pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader.cinit() pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source() FileNotFoundError: [Errno 2] File ../covid-chestxray-dataset/metadata.csv does not exist: '../covid-chestxray-dataset/metadata.csv'

FileNotFoundError Traceback (most recent call last) in 1 # adapted from https://github.com/mlmed/torchxrayvision/blob/master/torchxrayvision/datasets.py#L814----> 2 cohen_csv = pd.read_csv(cohen_csvpath, nrows=None) 3 #idx_pa = csv["view"] == "PA" # Keep only the PA view 4 views = ["PA", "AP", "AP Supine", "AP semi erect", "AP erect"] 5 cohen_idx_keep = cohen_csv.view.isin(views) ~\anaconda3\lib\site-packages\pandas\io\parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision) 674 ) 675 --> 676 return _read(filepath_or_buffer, kwds) 677 678 parser_f.name = name ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _read(filepath_or_buffer, kwds) 446 447 # Create the parser.--> 448 parser = TextFileReader(fp_or_buf, kwds) 449 450 if chunksize or iterator: ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, f, engine, kwds) 878 self.options["has_index_names"] = kwds["has_index_names"] 879 --> 880 self._make_engine(self.engine) 881 882 def close(self): ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _make_engine(self, engine) 1112 def _make_engine(self, engine="c"): 1113 if engine == "c":-> 1114 self._engine = CParserWrapper(self.f, self.options) 1115 else: 1116 if engine == "python": ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, src, kwds) 1889 kwds["usecols"] = self.usecols 1890 -> 1891 self._reader = parsers.TextReader(src, **kwds) 1892 self.unnamed_cols = self._reader.unnamed_cols 1893 pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader.cinit() pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source() FileNotFoundError: [Errno 2] File ../covid-chestxray-dataset/metadata.csv does not exist: '../covid-chestxray-dataset/metadata.csv'

FileNotFoundError Traceback (most recent call last) in 1 # adapted from https://github.com/mlmed/torchxrayvision/blob/master/torchxrayvision/datasets.py#L814----> 2 cohen_csv = pd.read_csv(cohen_csvpath, nrows=None) 3 #idx_pa = csv["view"] == "PA" # Keep only the PA view 4 views = ["PA", "AP", "AP Supine", "AP semi erect", "AP erect"] 5 cohen_idx_keep = cohen_csv.view.isin(views) ~\anaconda3\lib\site-packages\pandas\io\parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision) 674 ) 675 --> 676 return _read(filepath_or_buffer, kwds) 677 678 parser_f.name = name ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _read(filepath_or_buffer, kwds) 446 447 # Create the parser.--> 448 parser = TextFileReader(fp_or_buf, kwds) 449 450 if chunksize or iterator: ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, f, engine, kwds) 878 self.options["has_index_names"] = kwds["has_index_names"] 879 --> 880 self._make_engine(self.engine) 881 882 def close(self): ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _make_engine(self, engine) 1112 def _make_engine(self, engine="c"): 1113 if engine == "c":-> 1114 self._engine = CParserWrapper(self.f, self.options) 1115 else: 1116 if engine == "python": ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, src, kwds) 1889 kwds["usecols"] = self.usecols 1890 -> 1891 self._reader = parsers.TextReader(src, **kwds) 1892 self.unnamed_cols = self._reader.unnamed_cols 1893 pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader.cinit() pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source() FileNotFoundError: [Errno 2] File ../covid-chestxray-dataset/metadata.csv does not exist: '../covid-chestxray-dataset/metadata.csv'

FileNotFoundError Traceback (most recent call last) in 1 # adapted from https://github.com/mlmed/torchxrayvision/blob/master/torchxrayvision/datasets.py#L814----> 2 cohen_csv = pd.read_csv(cohen_csvpath, nrows=None) 3 #idx_pa = csv["view"] == "PA" # Keep only the PA view 4 views = ["PA", "AP", "AP Supine", "AP semi erect", "AP erect"] 5 cohen_idx_keep = cohen_csv.view.isin(views) ~\anaconda3\lib\site-packages\pandas\io\parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision) 674 ) 675 --> 676 return _read(filepath_or_buffer, kwds) 677 678 parser_f.name = name ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _read(filepath_or_buffer, kwds) 446 447 # Create the parser.--> 448 parser = TextFileReader(fp_or_buf, kwds) 449 450 if chunksize or iterator: ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, f, engine, kwds) 878 self.options["has_index_names"] = kwds["has_index_names"] 879 --> 880 self._make_engine(self.engine) 881 882 def close(self): ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _make_engine(self, engine) 1112 def _make_engine(self, engine="c"): 1113 if engine == "c":-> 1114 self._engine = CParserWrapper(self.f, self.options) 1115 else: 1116 if engine == "python": ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, src, kwds) 1889 kwds["usecols"] = self.usecols 1890 -> 1891 self._reader = parsers.TextReader(src, **kwds) 1892 self.unnamed_cols = self._reader.unnamed_cols 1893 pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader.cinit() pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source() FileNotFoundError: [Errno 2] File ../covid-chestxray-dataset/metadata.csv does not exist: '../covid-chestxray-dataset/metadata.csv'

FileNotFoundError Traceback (most recent call last) in 1 # adapted from https://github.com/mlmed/torchxrayvision/blob/master/torchxrayvision/datasets.py#L814----> 2 cohen_csv = pd.read_csv(cohen_csvpath, nrows=None) 3 #idx_pa = csv["view"] == "PA" # Keep only the PA view 4 views = ["PA", "AP", "AP Supine", "AP semi erect", "AP erect"] 5 cohen_idx_keep = cohen_csv.view.isin(views) ~\anaconda3\lib\site-packages\pandas\io\parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision) 674 ) 675 --> 676 return _read(filepath_or_buffer, kwds) 677 678 parser_f.name = name ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _read(filepath_or_buffer, kwds) 446 447 # Create the parser.--> 448 parser = TextFileReader(fp_or_buf, kwds) 449 450 if chunksize or iterator: ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, f, engine, kwds) 878 self.options["has_index_names"] = kwds["has_index_names"] 879 --> 880 self._make_engine(self.engine) 881 882 def close(self): ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _make_engine(self, engine) 1112 def _make_engine(self, engine="c"): 1113 if engine == "c":-> 1114 self._engine = CParserWrapper(self.f, self.options) 1115 else: 1116 if engine == "python": ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, src, kwds) 1889 kwds["usecols"] = self.usecols 1890 -> 1891 self._reader = parsers.TextReader(src, **kwds) 1892 self.unnamed_cols = self._reader.unnamed_cols 1893 pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader.cinit() pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source() FileNotFoundError: [Errno 2] File ../covid-chestxray-dataset/metadata.csv does not exist: '../covid-chestxray-dataset/metadata.csv'

FileNotFoundError Traceback (most recent call last) in 1 # adapted from https://github.com/mlmed/torchxrayvision/blob/master/torchxrayvision/datasets.py#L814----> 2 cohen_csv = pd.read_csv(cohen_csvpath, nrows=None) 3 #idx_pa = csv["view"] == "PA" # Keep only the PA view 4 views = ["PA", "AP", "AP Supine", "AP semi erect", "AP erect"] 5 cohen_idx_keep = cohen_csv.view.isin(views) ~\anaconda3\lib\site-packages\pandas\io\parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision) 674 ) 675 --> 676 return _read(filepath_or_buffer, kwds) 677 678 parser_f.name = name ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _read(filepath_or_buffer, kwds) 446 447 # Create the parser.--> 448 parser = TextFileReader(fp_or_buf, kwds) 449 450 if chunksize or iterator: ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, f, engine, kwds) 878 self.options["has_index_names"] = kwds["has_index_names"] 879 --> 880 self._make_engine(self.engine) 881 882 def close(self): ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _make_engine(self, engine) 1112 def _make_engine(self, engine="c"): 1113 if engine == "c":-> 1114 self._engine = CParserWrapper(self.f, self.options) 1115 else: 1116 if engine == "python": ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, src, kwds) 1889 kwds["usecols"] = self.usecols 1890 -> 1891 self._reader = parsers.TextReader(src, **kwds) 1892 self.unnamed_cols = self._reader.unnamed_cols 1893 pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader.cinit() pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source() FileNotFoundError: [Errno 2] File ../covid-chestxray-dataset/metadata.csv does not exist: '../covid-chestxray-dataset/metadata.csv'

this is the error which I am getting while running 1 of my code cell there are other errors too

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On Thu, Jun 18, 2020 at 12:59 AM Sania Hafeez saniahafeez1990@gmail.com wrote:

okay let me try it again or copy error here

https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon Virus-free. www.avast.com https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link <#m_-7516481418729131348_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Thu, Jun 18, 2020 at 12:57 AM Javier G. Montoya S. < notifications@github.com> wrote:

We can't see the images you're sending, I think using the web interface instead of replying via email should work

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-645591111, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQUZDPFF5OOTKKBHNHDRXEN4HANCNFSM4NPIANKQ .

-- Thanks Sania

-- Thanks Sania

[sanh642]

FileNotFoundError Traceback (most recent call last) in 1 # adapted from https://github.com/mlmed/torchxrayvision/blob/master/torchxrayvision/datasets.py#L814----> 2 cohen_csv = pd.read_csv(cohen_csvpath, nrows=None) 3 #idx_pa = csv["view"] == "PA" # Keep only the PA view 4 views = ["PA", "AP", "AP Supine", "AP semi erect", "AP erect"] 5 cohen_idx_keep = cohen_csv.view.isin(views) ~\anaconda3\lib\site-packages\pandas\io\parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision) 674 ) 675 --> 676 return _read(filepath_or_buffer, kwds) 677 678 parser_f.name = name ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _read(filepath_or_buffer, kwds) 446 447 # Create the parser.--> 448 parser = TextFileReader(fp_or_buf, kwds) 449 450 if chunksize or iterator: ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, f, engine, kwds) 878 self.options["has_index_names"] = kwds["has_index_names"] 879 --> 880 self._make_engine(self.engine) 881 882 def close(self): ~\anaconda3\lib\site-packages\pandas\io\parsers.py in _make_engine(self, engine) 1112 def _make_engine(self, engine="c"): 1113 if engine == "c":-> 1114 self._engine = CParserWrapper(self.f, self.options) 1115 else: 1116 if engine == "python": ~\anaconda3\lib\site-packages\pandas\io\parsers.py in init(self, src, kwds) 1889 kwds["usecols"] = self.usecols 1890 -> 1891 self._reader = parsers.TextReader(src, **kwds) 1892 self.unnamed_cols = self._reader.unnamed_cols 1893 pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader.cinit() pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source() FileNotFoundError: [Errno 2] File ../covid-chestxray-dataset/metadata.csv does not exist: '../covid-chestxray-dataset/metadata.csv'

https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon Virus-free. www.avast.com https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Thu, Jun 18, 2020 at 12:59 AM Sania Hafeez saniahafeez1990@gmail.com wrote:

okay let me try it again or copy error here

https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon Virus-free. www.avast.com https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=link <#m_-7516481418729131348_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Thu, Jun 18, 2020 at 12:57 AM Javier G. Montoya S. < notifications@github.com> wrote:

We can't see the images you're sending, I think using the web interface instead of replying via email should work

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-645591111, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQUZDPFF5OOTKKBHNHDRXEN4HANCNFSM4NPIANKQ .

-- Thanks Sania

-- Thanks Sania

[jgmontoya]

You need to download the different datasets before running the script (as explained here)

[sanh642]

I downloaded all sets and uploaded in my jupyter and then I run

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On Thu, Jun 18, 2020 at 1:47 AM Javier G. Montoya S. < notifications@github.com> wrote:

You need to download the different datasets before running the script (as explained here https://github.com/lindawangg/COVID-Net/blob/master/docs/COVIDx.md)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lindawangg/COVID-Net/issues/74#issuecomment-645616097, or unsubscribe https://github.com/notifications/unsubscribe-auth/APZGFQT6BOGG2HCVSL6G5ADRXETW5ANCNFSM4NPIANKQ .

-- Thanks Sania

[ankitdata]

Hi @jgmontoya

I am trying run eval.py, so here inside data/test folder which test data i should add.?

https://github.com/lindawangg/COVID-Net/blob/fd532e7792e6bc474d0de1a615ba82b87d1cae4d/eval.py#L46

Thanks .

[jgmontoya]

Hi,

My understanding is that in data/test you should have the files specified in the testfile (i.e. "test_COVIDx3.txt").