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jjhelmus / nmrglue

A module for working with NMR data in Python
BSD 3-Clause "New" or "Revised" License
209 stars 86 forks source link

Reading bruker fid file TypeError #115

Closed Lee4396 closed 4 years ago

Lee4396 commented 4 years ago

When I tried to read raw fid file I got this weird type error

TypeError Traceback (most recent call last)

in ----> 1 dic,data = ng.bruker.read(dir='./Lee_NMR/S_20190122_00439/1/', bin_file='fid') c:\users\zwqy\appdata\local\programs\python\python38\lib\site-packages\nmrglue\fileio\bruker.py in read(dir, bin_file, acqus_files, pprog_file, shape, cplex, big, read_pulseprogram, read_acqus) 325 standard files. 326 read_procs : bool, optional --> 327 True to read procs files(s), False prevents reading. 328 329 Returns c:\users\zwqy\appdata\local\programs\python\python38\lib\site-packages\nmrglue\fileio\bruker.py in read_binary(filename, shape, cplex, big) 994 995 # extract data type from dictionary --> 996 try: 997 dtypa = int(dic["acqus"]["DTYPA"]) 998 except KeyError: TypeError: 'float' object cannot be interpreted as an integer No clue what's going on here
kaustubhmote commented 4 years ago

I can reproduce this with version 0.5, but seems like this issue was fixed in version 0.6. This is an error associated with non-integer division in calculating the number of data points. It got taken care of in a rehaul of the bruker.read function (offending line 397 in bruker.py in v0.5). Previous versions of numpy allowed this, but not anymore. If you are using a version older than 0.6, the best way to fix this is to update to the latest version of nmrglue.

pip install nmrglue should update you to version 0.7, and pip install git+https://github.com/jjhelmus/nmrglue.git should update you to the current development version.

Lee4396 commented 4 years ago

True, I updated to 0.7 and fixed the problem. Pre-assigning a value to shape also fixes the problem.