for loop over D.query_iter(D.ms1_frames, columns=('intensity',)) crashed

animesh commented 3 years ago

I am running it over a window2016server machine with 128GB RAM where the following works

path = Path(pathFiles)
D = OpenTIMS(path) # get data handle
print(pathFiles,D) #print(len(D)) # The number of peaks.
OpenTIMS(1634400182)
pprint(D.query(frames=[1], columns=all_columns))
{'frame': array([1, 1, 1, ..., 1, 1, 1], dtype=uint32),
'intensity': array([21, 54, 54, ..., 22, 61, 81], dtype=uint32),
'inv_ion_mobility': array([1.59926563, 1.59485905, 1.59045181, ..., 0.60113621, 0.60113621,
       0.60113621]),
'mz': array([1377.64799752, 1436.23477832, 1613.74566582, ...,  515.79462555,
        629.21372085,  801.32747883]),
'retention_time': array([0.456886, 0.456886, 0.456886, ..., 0.456886, 0.456886, 0.456886]),
'scan': array([ 35,  39,  43, ..., 926, 926, 926], dtype=uint32),
'tof': array([343878, 353782, 382616, ..., 161198, 191291, 232170], dtype=uint32)}

but following crashes after few loops

for fr in D.query_iter(D.ms1_frames, columns=('intensity',)):
    print(fr['intensity'])

is there a way to know what is the underlying issue?

MatteoLacki commented 3 years ago

Hello,

Not if you don't supply error messages :) And the version of opentims!

Best,

Mateusz Krzysztof Łącki

German tel. +49 159 01681376 Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki

On Fri, Sep 3, 2021 at 4:26 PM Ani @.***> wrote:

I am running it over a window2016server machine with 128GB RAM where the following works

path = Path(pathFiles) D = OpenTIMS(path) # get data handle print(pathFiles,D) #print(len(D)) # The number of peaks. OpenTIMS(1634400182) pprint(D.query(frames=[1], columns=all_columns)) {'frame': array([1, 1, 1, ..., 1, 1, 1], dtype=uint32), 'intensity': array([21, 54, 54, ..., 22, 61, 81], dtype=uint32), 'inv_ion_mobility': array([1.59926563, 1.59485905, 1.59045181, ..., 0.60113621, 0.60113621, 0.60113621]), 'mz': array([1377.64799752, 1436.23477832, 1613.74566582, ..., 515.79462555, 629.21372085, 801.32747883]), 'retention_time': array([0.456886, 0.456886, 0.456886, ..., 0.456886, 0.456886, 0.456886]), 'scan': array([ 35, 39, 43, ..., 926, 926, 926], dtype=uint32), 'tof': array([343878, 353782, 382616, ..., 161198, 191291, 232170], dtype=uint32)}

but following crashes after few loops

for fr in D.query_iter(D.ms1_frames, columns=('intensity',)): print(fr['intensity'])

is there a way to know what is the underlying issue?

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liquidcarbon commented 3 years ago

The issue could be rooted here:

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
/tmp/ipykernel_28411/1257180327.py in <module>
----> 1 D.query(frames=73, columns=('intensity'))

~ ... python3.9/site-packages/opentimspy/opentims.py in query(self, frames, columns)
    140             dict: columns to numpy array mapping.
    141         """
--> 142         assert all(c in self.all_columns for c in columns), f"Accepted column names: {self.all_columns}"
    143 
    144         try:

AssertionError: Accepted column names: ('frame', 'scan', 'tof', 'intensity', 'mz', 'inv_ion_mobility', 'retention_time')

Using columns=('intensity',) should've worked, but using ('intensity') (without the comma) will fail. Perhaps this finickity could be addressed

alima82 commented 2 years ago

This code is fake! I can't plot_intensity_given_mz_inv_ion_mobility. it does NOT work at all. I wrote J prot Res to inform they have been publishing unfinished/fake bioinformatics work.