Fix timecourse extraction code to properly generate labelled index ac…

…counting for cells that can not be extracted as being too close to slide edges

final fix for issues resulting in "empty" cells without proper labelling being generated

src/sparcscore/pipeline/extraction.py

@@ -781,7 +781,7 @@ def _transfer_tempmmap_to_hdf5(self):
 
  #generate index data container
  index_labelled = _tmp_single_cell_index[keep_index]
- index_labelled = pd.DataFrame(index_labelled)[1:].reset_index().values #need to reset the lookup index so that it goes up sequentially
+ index_labelled = pd.DataFrame(index_labelled).iloc[:, 1:].reset_index(drop = True).values #need to reset the lookup index so that it goes up sequentially
  index_labelled = np.char.encode(index_labelled.astype(str))
 
  hf.create_dataset('single_cell_index_labelled', data = index_labelled, chunks = None, dtype = dt)
@@ -807,8 +807,7 @@ def _transfer_tempmmap_to_hdf5(self):
  with h5py.File(self.output_path, 'a') as hf:
 
  #need to save this index seperately since otherwise we get issues with the classificaiton of the extracted cells
- index = _tmp_single_cell_index[keep_index, 0:2]
- _, cell_ids = index.T
+ cell_ids = _tmp_single_cell_index[keep_index, 1]
  index = np.array(list(zip(range(len(cell_ids)), cell_ids)))
  index = index.astype("uint64")