Bug #1051
closedError when trying to do Helical Insert in Manual Picker
0%
Description
Manual picker is not working for picking filaments. See the error message below. Also, my images were uploaded (not collected on leginon) and are rectangles (13176x8964). They get rescaled in manual picker (to 13176x8960), and the whole micrograph shows up for particle picking, but it is preventing me from selecting particles outside of an imaginary 8960x8960 box. This severely limits my data selection and is a big problem for people with rectangular images.
COMMAND:
/ami/sw/bin/appion manualpicker.py --projectid=277 --preset=upload --session=10nov19z --runname=manrun1 --rundir=/ami/data00/appion/10nov19z/extract/manrun1 --no-rejects --no-wait --commit --limit=2 --continue --median=2 --lowpass=15 --highpass=0 --planereg --bin=8 --diam=330 --pixlimit=4.0 --shape=plus --shapesize=16
OUTPUT/ERROR MESSAGE:
Beginning Main Loop
Starting image 1 ( skip:0, remain:1 ) id:1388369, file: 10nov19z_a4397
... Pixel size: 1.8
... reading filtered image from mrc file
Traceback (most recent call last):
File "/ami/sw/packages/myami-2.1/appion/bin/manualpicker.py", line 290, in onHelicalInsert
targets = self.panel.getTargets('Select Particles')
File "/ami/sw/packages/myami-2.1/leginon/gui/wx/TargetPanel.py", line 81, in getTargets
return self._getSelectionTool().getTargets(name)
File "/ami/sw/packages/myami-2.1/leginon/gui/wx/SelectionTool.py", line 177, in getTargets
return self._getTypeTool(name).targettype.getTargets()
File "/ami/sw/packages/myami-2.1/leginon/gui/wx/SelectionTool.py", line 101, in _getTypeTool
raise ValueError('No type \'%s\' added' % name)
ValueError: No type 'Select Particles' added
Updated by Neil Voss over 13 years ago
There appear to be 3 separate bugs here.
I fixed something similar to this at least in TiltPicker where the limits of x and y were swapped see #418, so it appears you are limited to a box, but it is actually a rectangle in the wrong direction. I missed this fix in manualpicker, so it is fixed now in r15062.
The pixel dimension might be because they are not divisible by 8, but I don't know why that would be, if you are not binning.
Lauren, are saying there is a another bug with the insert button? There appears to be some configuration with the picking tool error in the traceback that I cannot diagnose without testing.
Updated by Anchi Cheng over 13 years ago
- Status changed from New to In Code Review
- Assignee changed from Anchi Cheng to Lauren Fisher
r15063 fixed the onHelicalInsert part of the bug. It was caused by removing target type "Select Particles" when I added the labeled particle picking feature. You should be able to pick two kinds of helices, too, if you like. Also found that the stepsize is determined wrong, so I fixed that. I also popped the start point duplicate from the points that is to be set to target again.
Lauren, the last target point from the original target list is now added to the end if the step filling does not include it. This does make the step uneven at the end point. If this is not the preferred behavior, you can remove it from the code. I was not sure which way it should be.
Updated by Lauren Fisher over 13 years ago
- Status changed from In Code Review to In Test
Updated by Lauren Fisher over 13 years ago
- Status changed from In Test to Closed
Neil, Thank you for fixing the x and y limits. The rescaling is not an issue since it only knocks off a few pixels. I was binning by 8 and I understand that the final array size must be an even number.
Anchi, Thank you for fixing Helical Insert. I will leave the code as is for now, with the last target point included, since it can easily be removed by the user if they don't want it. I will discuss this with other helical users and if no one wants the last target point, I will remove it from the code at that point. I will also add an issue for updating the php code to include the --helicalstep parameter.
On a side note, I will be adding a feature request for manual picker to select nonorthogonal filament boxes based on the filament axis. For helical processing using phoelix scripts the filaments must be either vertical or horizontal in the box. As it is now the filaments get boxed out at all different angles and this is problematic for me. I have a workaround, but ultimately it would be nice to have this feature in the pipeline for helical processing.
Thank you both for your help!