Hi all!
I am getting a 'No objects to concatenate' error when trying to use the pipeline. I have already checked the zipped .mcd-files and the panel-.csv-file multiple times and also the directories but I just cannot resolve the issue...
I would really appreciate the help! Thank you very much!
Below I have attached the respective screenshots. Following is the error text:
Generate a csv with all the acquisition metadata
The csv file can be found in the data/cpout folder
exportacquisitioncsv.export_acquisition_csv(folder_ome, fol_out=folder_cp)
ValueError Traceback (most recent call last)
in
----> 1 exportacquisitioncsv.export_acquisition_csv(folder_ome, fol_out=folder_cp)
~\anaconda3\envs\imctools\lib\site-packages\imctools\scripts\exportacquisitioncsv.py in export_acquisition_csv(fol_ome, fol_out, outname)
34 if outname is None:
35 outname=AC_META
---> 36 dat_meta = read_acmeta(fol_ome)
37 dat_meta.to_csv(os.path.join(fol_out, outname+SUF_CSV), index=False)
38
~\anaconda3\envs\imctools\lib\site-packages\imctools\scripts\exportacquisitioncsv.py in read_acmeta(fol_ome)
28
29 def read_acmeta(fol_ome):
---> 30 dat_acmeta = _read_and_concat(fol_ome, SUFFIX_ACMETA, COL_ACID)
31 return dat_acmeta
32
~\anaconda3\envs\imctools\lib\site-packages\imctools\scripts\exportacquisitioncsv.py in _read_and_concat(fol_ome, suffix, idname)
21 ac_names = os.listdir(fol_ome)
22 dat = pd.concat([pd.read_csv(os.path.join(fol_ome, a, a+suffix)) for a in ac_names],
---> 23 keys=ac_names, names=[COL_ACSESSION, VAL_TEMP])
24 dat = dat.reset_index(VAL_TEMP, drop=True)
25 dat = dat.reset_index()
~\anaconda3\envs\imctools\lib\site-packages\pandas\core\reshape\concat.py in concat(objs, axis, join, ignore_index, keys, levels, names, verify_integrity, sort, copy)
282 verify_integrity=verify_integrity,
283 copy=copy,
--> 284 sort=sort,
285 )
286
~\anaconda3\envs\imctools\lib\site-packages\pandas\core\reshape\concat.py in init(self, objs, axis, join, keys, levels, names, ignore_index, verify_integrity, copy, sort)
329
330 if len(objs) == 0:
--> 331 raise ValueError("No objects to concatenate")
332
333 if keys is None:
ValueError: No objects to concatenate
![Screenshot 2020-10-29 113917](https://user-images.githubusercontent.com/73642795/97557770-84b63d00-19db-11eb-8712-b0b5bc14f7aa.jpg)
![Screenshot 2020-10-29 113955](https://user-images.githubusercontent.com/73642795/97557781-87189700-19db-11eb-8f52-ad6ac6161d4e.jpg)