Cxi02416 calibration - Revision history

Aaron: /* Refine metrology (v3) */

2016-05-18T23:55:15Z

Refine metrology (v3)

← Older revision		Revision as of 23:55, 18 May 2016
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	== Refine metrology (v3) ==		== Refine metrology (v3) ==

	We now refine the metrology generated from the indexed images from trial 3 and call it metrology version 3 (v3). Now that we have a better ~~idea~~ of the unit cell, we ~~add~~ a phil file ~~with~~ a restraint for ~~all~~ the crystals ~~to that unit cell~~. We also increase the number images used to 2000.		We now refine the metrology generated from the indexed images from trial 3 and call it metrology version 3 (v3). Now that we have a better estimate of the unit cell, we [[cxi02416-refine.phil \| use a phil file]] that adds a restraint to the joint refinement such the refined unit cells for each crystal have a similar set of dimensions. This assumes the crystals are isomorphous. We also increase the number images used to 2000.

	bsub -q psanaq -o t001_2k.out '''cspad.cbf_metrology''' tag=t001_2k \		bsub -q psanaq -o t001_2k.out '''cspad.cbf_metrology''' tag=t001_2k \
	[[cxi02416-refine.phil]] reflections=indexed ../r0*/001/out \		[[cxi02416-refine.phil]] reflections=indexed ../r0*/001/out \
	n_subset=2000 split_dataset=True		n_subset=2000 split_dataset=True

	Now that we have a good estimate of the unit cell, we use [[cxi02416-refine.phil \| a refinement phil file]], to add a restraint to the joint refinement such the refined unit cells for each crystal have a similar set of dimensions. This assumes the crystals are isomorphous.

	After refinement, use '''cxi.display_metrology''', '''dev.dials.plot_detector_shifts''', and/or '''cspad.detector_shifts''' to evaluate how much the tiles moved:		After refinement, use '''cxi.display_metrology''', '''dev.dials.plot_detector_shifts''', and/or '''cspad.detector_shifts''' to evaluate how much the tiles moved:

Aaron: /* Index using v2 metrology */

2016-05-18T23:52:23Z

Index using v2 metrology

← Older revision		Revision as of 23:52, 18 May 2016
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	mp.nproc=36 mp.queue=psanaq output.split_logs=True \		mp.nproc=36 mp.queue=psanaq output.split_logs=True \
	input.dispatcher=cctbx.xfel.xtc_process \		input.dispatcher=cctbx.xfel.xtc_process \
	input.target=cxi02416/lyso-t001.phil input.trial=1 input.run_num=$i \		input.target=[[cxi02416-lyso-t001.phil]] input.trial=1 input.run_num=$i \
	input.cfg=cxi02416-calibdir.cfg; done		input.cfg=cxi02416-calibdir.cfg; done

Aaron: /* Initial indexing */

2016-05-18T23:51:18Z

Initial indexing

← Older revision		Revision as of 23:51, 18 May 2016
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	mp.nproc=36 mp.queue=psanaq output.split_logs=True \		mp.nproc=36 mp.queue=psanaq output.split_logs=True \
	input.dispatcher=cctbx.xfel.xtc_process \		input.dispatcher=cctbx.xfel.xtc_process \
	input.target=cxi02416-lyso-t000.phil input.trial=0 \		input.target=[[cxi02416-lyso-t000.phil]] input.trial=0 \
	input.run_num=$i; done		input.run_num=$i; done

Aaron: /* Refine metrology (v3) */

2016-05-18T23:50:09Z

Refine metrology (v3)

← Older revision		Revision as of 23:50, 18 May 2016
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	bsub -q psanaq -o t001_2k.out '''cspad.cbf_metrology''' tag=t001_2k \		bsub -q psanaq -o t001_2k.out '''cspad.cbf_metrology''' tag=t001_2k \
	cxi02416-refine.phil reflections=indexed ../r0*/001/out \		[[cxi02416-refine.phil]] reflections=indexed ../r0*/001/out \
	n_subset=2000 split_dataset=True		n_subset=2000 split_dataset=True

Aaron: /* Refine metrology (v3) */

2016-05-18T23:47:38Z

Refine metrology (v3)

← Older revision		Revision as of 23:47, 18 May 2016
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	cxi02416-refine.phil reflections=indexed ../r0*/001/out \		cxi02416-refine.phil reflections=indexed ../r0*/001/out \
	n_subset=2000 split_dataset=True		n_subset=2000 split_dataset=True

			Now that we have a good estimate of the unit cell, we use [[cxi02416-refine.phil \| a refinement phil file]], to add a restraint to the joint refinement such the refined unit cells for each crystal have a similar set of dimensions. This assumes the crystals are isomorphous.

	After refinement, use '''cxi.display_metrology''', '''dev.dials.plot_detector_shifts''', and/or '''cspad.detector_shifts''' to evaluate how much the tiles moved:		After refinement, use '''cxi.display_metrology''', '''dev.dials.plot_detector_shifts''', and/or '''cspad.detector_shifts''' to evaluate how much the tiles moved:

Aaron: /* Index using v2 metrology */

2016-05-18T23:35:58Z

Index using v2 metrology

← Older revision		Revision as of 23:35, 18 May 2016
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	input.cfg=cxi02416-calibdir.cfg; done		input.cfg=cxi02416-calibdir.cfg; done

	~~The input phil file is the same as before, with one exception (see below). However, to~~ instruct psana to use the modified calibration directory, we add a psana config file named cxi02416-calibdir.cfg with these lines:		To instruct psana to use the modified calibration directory, we add a psana config file named cxi02416-calibdir.cfg with these lines:

	[psana]		[psana]
Line 401:		Line 401:

	If you have write permissions to your geometry folder, you don't need to use this config file or make a copy of your calibration directory. We recommend saving the original metrology like we did in the above example, by renaming it to 0-end.data.v1, so you can return to it as needed.		If you have write permissions to your geometry folder, you don't need to use this config file or make a copy of your calibration directory. We recommend saving the original metrology like we did in the above example, by renaming it to 0-end.data.v1, so you can return to it as needed.

			The [[cxi02416-lyso-t001.phil \| input phil file]] is the same as before, with a slight change to the unit cell dimensions. The program '''cspad.detector_statistics''' (described below) reports an average unit cell after joint refinement, which we use to update our indexing cell target.

	Indexing with the new metrology yielded 5305 indexed images.		Indexing with the new metrology yielded 5305 indexed images.

Aaron: /* Further indexing and refinement (v4) */

2016-05-18T16:21:09Z

Further indexing and refinement (v4)

← Older revision		Revision as of 16:21, 18 May 2016
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	</div>		</div>

	The fast and slow offset sigmas are lower generally, but not substantially. 5475 images were indexed, ~~a small~~ increase of ~~0.X~~% over v3 metrology. ~~Further, the~~ change in tile position is minimal, as shown by '''cspad.detector_shifts''' (delta XY movements (microns): detector: 1.5, quadrants: 4.0+/2.3, sensors: 5.5+/-5.9). The metrology has likely converged.		The fast and slow offset sigmas are lower generally, but not substantially. 5475 images were indexed, an increase of 1% over v3 metrology. The change in tile position is minimal, as shown by '''cspad.detector_shifts''' (delta XY movements (microns): detector: 1.5, quadrants: 4.0+/2.3, sensors: 5.5+/-5.9). The metrology has likely converged.

	== Deploy metrology ==		== Deploy metrology ==

	v4 metrology is now ready for use. Deploy it or use it directly for indexing as described in [[Cxi0216 calibration#Index using v2 metrology \| indexing using v2 metrology]].		v4 metrology is now ready for use. Deploy it or use it directly for indexing as described in [[Cxi0216 calibration#Index using v2 metrology \| indexing using v2 metrology]].

Aaron: /* Further indexing and refinement (v4) */

2016-05-18T16:19:21Z

Further indexing and refinement (v4)

Show changes

Aaron: /* Evaluate metrology */

2016-05-13T23:30:17Z

Evaluate metrology

Show changes

Aaron: /* Refine metrology (v3) */

2016-05-13T22:52:12Z

Refine metrology (v3)

← Older revision		Revision as of 22:52, 13 May 2016
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	== Refine metrology (v3) ==		== Refine metrology (v3) ==

	We now refine the metrology generated from the indexed images from trial 3 and call it metrology version 3 (v3). ~~The command is otherwise~~ the ~~same~~, with ~~an updated tag~~. We also increase the number images used to 2000.		We now refine the metrology generated from the indexed images from trial 3 and call it metrology version 3 (v3). Now that we have a better idea of the unit cell, we add a phil file with a restraint for all the crystals to that unit cell. We also increase the number images used to 2000.

	bsub -q psanaq -o ~~t003_1k~~.out '''cspad.cbf_metrology''' tag=~~t003_1k~~ \		bsub -q psanaq -o t001_2k.out '''cspad.cbf_metrology''' tag=t001_2k \
	cxi02416-refine.phil reflections=indexed ../r0*/~~003~~/out \		cxi02416-refine.phil reflections=indexed ../r0*/001/out \
	n_subset=2000 split_dataset=True		n_subset=2000 split_dataset=True

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	'''cspad.detector_shifts''' \		'''cspad.detector_shifts''' \
	~~t002_1k_1_refined_experiments_level2~~.json ~~t002_1k_1_refined_reflections_level2~~.pickle \		t000_1k_1_refined_experiments_level2.json t000_1k_1_refined_reflections_level2.pickle \
	~~t003_2k_1_refined_experiments_level2~~.json ~~t003_2k_1_refined_reflections_level2~~.pickle		t001_2k_1_refined_experiments_level2.json t001_2k_1_refined_reflections_level2.pickle

	The Detector XY column shows the detector moved 5.8 microns in the XY plane, the quadrants on averaged moved 7.9+/- 4.0 microns and the 2x1 sensors moved 10.4+/-10.8 microns. The tile positions moved substantially less between v2 and v3 then they did between v1 and v2.		The Detector XY column shows the detector moved 4.3 microns in the XY plane, the quadrants on averaged moved 10.2 +/- 5.8 microns and the 2x1 sensors moved 11.7 +/- 11.5 microns. The tile positions moved substantially less between v2 and v3 then they did between v1 and v2.

	== Evaluate metrology ==		== Evaluate metrology ==