Unable read timsdata through TimsDIA class

[kishoret04]

I am able to read the data with TimsPyDF class

DIA_published_dir = <path with .d file >
data_published = TimsPyDF( DIA_published_dir)

But when I try reading it through TimsDIA class, I am getting below error. Following is the code used:

dia_data_pub = TimsDIA(DIA_published_dir)

KeyError Traceback (most recent call last)
~\Anaconda3\lib\site-packages\pandas\core\indexes\base.py in get_loc(self, key, method, tolerance)
2888 try:
-> 2889 return self._engine.get_loc(casted_key)
2890 except KeyError as err:

pandas_libs\index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas_libs\index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas_libs\hashtable_class_helper.pxi in pandas._libs.hashtable.Int64HashTable.get_item()

pandas_libs\hashtable_class_helper.pxi in pandas._libs.hashtable.Int64HashTable.get_item()

KeyError: -1

The above exception was the direct cause of the following exception:

KeyError Traceback (most recent call last)
in
1 DIA_published_dir = r'\VBOXSVR\UoH_DS\Summer 2020\Spectrometry lab internship\Project 2\Project2-RawData\DIAdata\20190710_HeLa_200ng_90min_diaPASEF_FastCE_py3_Slot1-1_1_46.d'
----> 2 dia_data_pub = TimsDIA(DIA_published_dir)

~\Anaconda3\lib\site-packages\timspy\timspy.py in init(self, analysis_directory, use_recalibrated_state)
672 W['left'] = np.searchsorted(self.grid, W.mz_left)
673 W['right'] = np.searchsorted(self.grid, W.mz_right)+1
--> 674 W['prev_left'] = [ W.left[-1] ]*2 + list(W.left[1:-1])
675 W['prev_right'] = [ W.right[-1] ]*2 + list(W.right[1:-1])
676 IM_windows = W[['scan_min','scan_max']].apply(lambda x: self.scanNumToOneOverK0(1,x))

~\Anaconda3\lib\site-packages\pandas\core\series.py in getitem(self, key)
880
881 elif key_is_scalar:
--> 882 return self._get_value(key)
883
884 if (

~\Anaconda3\lib\site-packages\pandas\core\series.py in _get_value(self, label, takeable)
989
990 # Similar to Index.get_value, but we do not fall back to positional
--> 991 loc = self.index.get_loc(label)
992 return self.index._get_values_for_loc(self, loc, label)
993

~\Anaconda3\lib\site-packages\pandas\core\indexes\multi.py in get_loc(self, key, method)
2698 if not isinstance(key, (tuple, list)):
2699 # not including list here breaks some indexing, xref #30892
-> 2700 loc = self._get_level_indexer(key, level=0)
2701 return _maybe_to_slice(loc)
2702

~\Anaconda3\lib\site-packages\pandas\core\indexes\multi.py in _get_level_indexer(self, key, level, indexer)
2963 else:
2964
-> 2965 code = self._get_loc_single_level_index(level_index, key)
2966
2967 if level > 0 or self.lexsort_depth == 0:

~\Anaconda3\lib\site-packages\pandas\core\indexes\multi.py in _get_loc_single_level_index(self, level_index, key)
2632 return -1
2633 else:
-> 2634 return level_index.get_loc(key)
2635
2636 def get_loc(self, key, method=None):

~\Anaconda3\lib\site-packages\pandas\core\indexes\base.py in get_loc(self, key, method, tolerance)
2889 return self._engine.get_loc(casted_key)
2890 except KeyError as err:
-> 2891 raise KeyError(key) from err
2892
2893 if tolerance is not None:

KeyError: -1

[MatteoLacki]

Hi, Try now, we have completely revised the code.

[pbjarterot]

Hi, I have the same issue now with python 3.10.6 and pandas 1.5.3

`
Traceback (most recent call last):
File "C:\Python310\lib\site-packages\pandas\core\indexes\base.py", line 3802, in get_loc
return self._engine.get_loc(casted_key)
File "pandas_libs\index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
File "pandas_libs\index.pyx", line 165, in pandas._libs.index.IndexEngine.get_loc
File "pandas_libs\hashtable_class_helper.pxi", line 2263, in pandas._libs.hashtable.Int64HashTable.get_item
File "pandas_libs\hashtable_class_helper.pxi", line 2273, in pandas._libs.hashtable.Int64HashTable.get_item
KeyError: -1

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "C:\Users\patbj751\Documents\GitHub\tims\testing_timspy.py", line 10, in
D = TimsPyDF(path) # get data handle
File "C:\Users\patbj751\AppData\Roaming\Python\Python310\site-packages\timspy\df.py", line 24, in init
self.frames_no = self.max_frame-self.min_frame+1
File "C:\Users\patbj751\AppData\Roaming\Python\Python310\site-packages\opentimspy\opentims.py", line 137, in max_frame
return self.frames["Id"][-1]
File "C:\Python310\lib\site-packages\pandas\core\series.py", line 981, in getitem
return self._get_value(key)
File "C:\Python310\lib\site-packages\pandas\core\series.py", line 1089, in _get_value
loc = self.index.get_loc(label)
File "C:\Python310\lib\site-packages\pandas\core\indexes\base.py", line 3804, in get_loc
raise KeyError(key) from err
KeyError: -1
`

[MatteoLacki]

Hello,

I think that the TimsPy does not stand the test of time and we gave much more attention to the simpler opentimspy project.
Nonetheless, I think it is as simple as using the TimsPyDF class instead of TimsPyDIA.
Retrospectively, I don't think there was a good point to complicate things and make a special subclass for DIA, as there are plenty DIA possible. For that I am sorry.

Best wishes,