search

DrSAR / SARlabpy

git clone git@pfeifer.phas.ubc.ca:SARlabpy (do not push to github, please)
http://code.SARlab.ca
Other
1 stars 0 forks source link

empty scans are loaded and appear as proper scans, they fail late in the process #40

Closed DrSAR closed 11 years ago

DrSAR commented 11 years ago

Before we tackle this: What is the problem? When would it be nice not to access a Scan only to find out that it's not there?

DrSAR commented 11 years ago

one suggestion: have Scan look at the existence of an fid before committing to loading.

DrSAR commented 11 years ago

try this out: check all scans that have an fid and see whether any of them DO NOT HAVE a acqp or method file.

DrSAR commented 11 years ago

OK - the most recent commit 6a76c355604561a adds a file that let's us quickly scan through all data directories in search of files that are not just so. The list below shows that most of the 9105 scans have everything. Quite a few have nothing (0) or only acqp+method (=1+2=3). 0 and 3 have been omitted.

Quite a few only have acqp (1) followed by the ones that have acqp+method+fid (7). Then there are three instances where fid is missing (=11) even though 2dseq is there!? Even though it's not as clear as you promised we could consider making it a policy to check for fid and accept that a scan is a scan if it's present, risking an exception for missing acqp and method (not found in our database).

You win.

$ python check_fid_acqp_method.py | egrep -v '[03]$' <21:02 PDT 13.03.>

Quick check for the presence of all sorts of BRUKER files in the entire dataroot. A fully stocked scan should have acqp, method, fid, 2dseq. This results in a score of

1 + 2 + 4 + 8 = 15. If one is missing, the score is less.

GdRelph3.ao2 / 5 : 1 herS3M09.3X1 / 13 : 7 MT4V01.9a3 / 7 : 7 readfidTest.ix1 / 99 : 7 MT5V03.9m1 / 6 : 7 MT5V04.9o1 / 6 : 7 SARTPZ2-19.MK1 / 3 : 11 HerS7Ss05.fC1 / 1 : 1 test001.9z1 / 1 : 1 HPGS4H03.6L1 / 28 : 7 Moosvi.ii1 / 14 : 1 NecS3Hs12.iM1 / 11 : 1 FlPhT101.9m1 / 23 : 7 MT5V01.9m1 / 7 : 7 MT3V01.9a1 / 7 : 7 HPGS4H06.6R1 / 28 : 7 HPGS6.iy1 / 8 : 11 NecS1Hs08.hk1 / 16 : 7 MT4V01.9a5 / 7 : 7 SARsusc02.Qb1 / 4 : 1 MT5V07.9z1 / 12 : 7 NecS3Hs04.iK2 / 12 : 7 SARperm0B.QZ1 / 8 : 7 SARgalbchi.Q51 / 12 : 11 gdwaterpha.PJ1 / 8 : 1 gdwaterpha.PJ1 / 7 : 1 MT4V01.9a2 / 7 : 7 herS3M08.4b1 / 14 : 7 herpil05.221 / 11 : 7 dummy.711 / 7 : 7 dummy.711 / 6 : 7 herS1Mo05.271 / 17 : 7 GdRelph4s4.ao2 / 8 : 1 SARperm2D.R71 / 2 : 11 SARGalbcal.Px1 / 1 : 1 013.iJ1 / 3 : 1 013.iJ1 / 4 : 1 Moosvi.ic1 / 1 : 1 herpil04.1V1 / 13 : 7 MT5V02.9m1 / 7 : 7 SARTPZ2-01.MJ1 / 8 : 7 SARperm1B.R61 / 8 : 7

MOUSETAIL3.9a1 / 1 : 1

9105 scans tested