Author: bugman
Date: Fri Oct 2 15:10:10 2015
New Revision: 27959
URL: http://svn.gna.org/viewcvs/relax?rev=27959&view=rev
Log:
Merged revisions
26913-26920,26957,27240,27244,27329,27552,27609-27611,27641-27653,27663,27715,27721,27806,27878-27899,27912
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r26913 | bugman | 2014-12-03 11:09:52 +0100 (Wed, 03 Dec 2014) | 7 lines
Expanded all of the Frame_order.test_simulate_* system tests.
Two atoms have been added to the origin [0, 0, 0], one in the moving
domain, the other in the
reference non-moving domain. The positions of these atoms are checked to
make sure that the domain
systems are correctly handled.
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r26914 | bugman | 2014-12-03 14:38:20 +0100 (Wed, 03 Dec 2014) | 3 lines
Expanded the double rotor model description in the frame_order.select_model
user function.
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r26915 | bugman | 2014-12-03 14:48:46 +0100 (Wed, 03 Dec 2014) | 5 lines
Added the pipe_name argument to the frame order check_model() function.
This is for the specific_analyses.frame_order.checks module.
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r26916 | bugman | 2014-12-03 15:08:26 +0100 (Wed, 03 Dec 2014) | 6 lines
Converted the specific_analyses.frame_order.checks module to the new Check
object design.
This follows from
http://wiki.nmr-relax.com/Relax_source_design#The_check_.2A.28.29_functions
and
the changes significantly simplify the checking objects.
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r26917 | bugman | 2014-12-03 15:11:46 +0100 (Wed, 03 Dec 2014) | 6 lines
Improved checking for the frame order generate_pivot() function.
The check_model() checking object is now called to make sure the frame
order model has been
specified, as this is essential for this function.
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r26918 | bugman | 2014-12-03 16:07:24 +0100 (Wed, 03 Dec 2014) | 6 lines
Created two system tests for the frame_order.simulate user function for the
double rotor model.
These are Frame_order.test_simulate_double_rotor_mode1_z_axis and
Frame_order.test_simulate_double_rotor_mode2_z_axis.
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r26919 | bugman | 2014-12-03 16:21:55 +0100 (Wed, 03 Dec 2014) | 6 lines
Created two system tests for the frame_order.simulate user function for the
double rotor model.
These are Frame_order.test_simulate_double_rotor_mode1_xz_plane_tilt and
Frame_order.test_simulate_double_rotor_mode2_xz_plane_tilt.
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r26920 | bugman | 2014-12-03 16:23:56 +0100 (Wed, 03 Dec 2014) | 7 lines
Added relax scripts which match the Frame_order.test_test_simulate_* system
tests.
These are the tests of the frame_order.simulate user function. These were
used to construct and
visually check the Brownian simulation and PDB model representation in a
molecular viewer. These
could be a useful reference, so have been added to the repository.
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r26957 | bugman | 2014-12-04 13:38:43 +0100 (Thu, 04 Dec 2014) | 3 lines
Removed a debugging printout.
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r27240 | bugman | 2015-01-20 14:54:07 +0100 (Tue, 20 Jan 2015) | 7 lines
Fix for the frame order auto-analysis when only the 'rigid' model is
optimised.
The final summary table printout for the number of Sobol' points used was
failing as there were no
models in the table. The table is now only printed out if non rigid models
are present in the model
list.
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r27244 | bugman | 2015-01-20 15:15:04 +0100 (Tue, 20 Jan 2015) | 3 lines
Copyright notice update to 2015 for the auto_analyses.frame_order module.
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r27329 | bugman | 2015-01-27 15:00:53 +0100 (Tue, 27 Jan 2015) | 7 lines
Introduced the nested_params_ave_dom_pos argument to the frame order
auto-analysis.
This allows the average domain position to be set to no rotations and
translations rather than
taking the average position from the rotor or free-rotor model. This can
be useful when large
motions are present causing the rigid model to have unreasonable domain
positions.
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r27552 | bugman | 2015-02-05 17:14:40 +0100 (Thu, 05 Feb 2015) | 6 lines
Fix for the frame_order.permute_axes user function description to allow the
manual to be compiled.
The table caption containing the user function name was causing the LaTeX
compilation to fail.
Therefore the captions have been rewritten to avoid the user function name.
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r27609 | bugman | 2015-02-09 13:45:17 +0100 (Mon, 09 Feb 2015) | 6 lines
Modified the frame order system test check_chi2() method to test the
statistics.model user function.
This causes all of the Frame_order.test_cam_* system tests to fail, as the
user function backend is
not implemented for the frame order analysis.
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r27610 | bugman | 2015-02-09 13:47:28 +0100 (Mon, 09 Feb 2015) | 6 lines
Implemented the frame order analysis backend for the statistics.model and
statistics.aic user functions.
This simply required aliasing the specific analysis API common
_get_model_container_cdp() method to
get_model_container().
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r27611 | bugman | 2015-02-09 15:29:08 +0100 (Mon, 09 Feb 2015) | 7 lines
Bug fix for the frame order specific analysis API base_data_loop() method.
This was looping over non-existent PCS and RDC data. Now the alignment ID
is checked for in the
interatomic data container 'rdc' data structure and the spin container
'pcs' data structure, as well
as values of None, before yielding the data.
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r27641 | bugman | 2015-02-14 10:38:26 +0100 (Sat, 14 Feb 2015) | 29 lines
Created a large set of system tests for implementing the
frame_order.distribute user function.
This user function will be similar to frame_order.simulate. However
instead of creating a PDB file
with models from a pseudo-Brownian simulation, the frame_order.distribute
user function will
generate a PDB file of models forming a uniform distribution of structures
covering the full frame
order motional space.
The new system tests are:
Frame_order.test_distribute_double_rotor_mode1_xz_plane_tilt
Frame_order.test_distribute_double_rotor_mode1_z_axis
Frame_order.test_distribute_double_rotor_mode2_xz_plane_tilt
Frame_order.test_distribute_double_rotor_mode2_z_axis
Frame_order.test_distribute_free_rotor_z_axis
Frame_order.test_distribute_iso_cone_z_axis
Frame_order.test_distribute_iso_cone_xz_plane_tilt
Frame_order.test_distribute_iso_cone_torsionless_z_axis
Frame_order.test_distribute_pseudo_ellipse_xz_plane_tilt
Frame_order.test_distribute_pseudo_ellipse_z_axis
Frame_order.test_distribute_pseudo_ellipse_free_rotor_z_axis
Frame_order.test_distribute_pseudo_ellipse_torsionless_z_axis
Frame_order.test_distribute_rotor_z_axis
These are aliases for the equivalent Frame_order.test_simulate_* system
tests which have had the
'type' keyword argument added, defaulting to 'sim', which allows to switch
between the
frame_order.simulate and frame_order.distribute user functions. The
concept behind these system
tests are the same for both user functions, so the code is shared.
........
r27642 | bugman | 2015-02-14 10:54:43 +0100 (Sat, 14 Feb 2015) | 6 lines
Created the front-end of the frame_order.distribute user function.
This is a copy and modification of the frame_order.simulate user function,
as the concepts are
similar.
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r27643 | bugman | 2015-02-14 10:56:30 +0100 (Sat, 14 Feb 2015) | 6 lines
Small modification of the frame_order.simulate user function.
The GUI file opening dialog wildcard selectors are now set to all PDB file
types (plain text, bzip2
compressed, and gzip compressed).
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r27644 | bugman | 2015-02-14 11:22:17 +0100 (Sat, 14 Feb 2015) | 6 lines
Added the frame_order.distribute user function to the auto-analysis results
output.
This will allow both the pseudo-Brownian simulation and uniform
distribution PDB files to be
available to the user in all results directories (excluding the
intermediate results for speed).
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r27645 | bugman | 2015-02-16 09:58:08 +0100 (Mon, 16 Feb 2015) | 9 lines
Implemented the back-end of the frame_order.distribute user function.
This follows the design of the pseudo-Brownian simulation
frame_order.simulate user function. The
specific_analyses.frame_order.uf.distribute() function has been created as
a modified copy of the
simulate() function of the same module. This simply performs checks and
assembles the data, passing
into the new lib.frame_order.simulate.uniform_distribution() function,
which itself is a modified
copy of the brownian() function in the same module.
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r27646 | bugman | 2015-02-16 10:08:49 +0100 (Mon, 16 Feb 2015) | 7 lines
Introduced the max_rotations argument into the frame_order.distribute user
function.
This is used to prevent the user function from running forever. This
happens whenever a cone
opening angle or torsion angle is zero, and hence the random sampling of
the rotational space will
never find rotations within the motional distribution.
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r27647 | bugman | 2015-02-16 10:19:33 +0100 (Mon, 16 Feb 2015) | 6 lines
Improved control of the frame_order.distribute user function in the frame
order auto-analysis.
The maximum number of rotations can now be set, and the argument for the
total states for the
distribution has been shortened.
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r27648 | bugman | 2015-02-16 10:23:43 +0100 (Mon, 16 Feb 2015) | 7 lines
Speed up of the Frame_order.test_auto_analysis system test.
After the introduction of the frame_order.distribute user function into the
auto-analysis, the test
was taking far too long to complete. Now the distribution arguments are
set to low values to allow
the test to pass in under a minute.
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r27649 | bugman | 2015-02-16 10:25:41 +0100 (Mon, 16 Feb 2015) | 6 lines
Changed the default relax results compression type to bzip2 in the frame
order auto-analysis.
This was set to no compression for speeding up some system tests, however
the system tests can set
this for themselves.
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r27650 | bugman | 2015-02-16 10:26:15 +0100 (Mon, 16 Feb 2015) | 3 lines
The Frame_order.test_auto_analysis system test now sets the results file
compression type to bzip2.
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r27651 | bugman | 2015-02-16 10:30:00 +0100 (Mon, 16 Feb 2015) | 5 lines
Changed the default max_rotations argument value to 100,000 in the
frame_order.distribute user function.
This decrease from one million is so the user function completes in a
reasonable amount of time.
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r27652 | bugman | 2015-02-16 10:35:33 +0100 (Mon, 16 Feb 2015) | 3 lines
The frame_order.distribute user function now warns when the maximum
rotations are reached.
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r27653 | bugman | 2015-02-16 10:36:57 +0100 (Mon, 16 Feb 2015) | 6 lines
Deleted a number of Frame_order.test_distribute* system tests.
These are the four double rotor model tests. The frame_order.distribute
user function cannot
operate on these test cases as one of the two torsion angles are set to
zero in the tests.
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r27663 | bugman | 2015-02-17 17:02:40 +0100 (Tue, 17 Feb 2015) | 6 lines
Fix to allow Monte Carlo simulations to be repeated in the frame order
analysis.
The code for checking for pre-existing Monte Carlo simulation data
structures and raising a
RelaxError if anything is found has been deleted.
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r27715 | bugman | 2015-02-24 09:34:36 +0100 (Tue, 24 Feb 2015) | 9 lines
Fix of a fatal bug preventing the frame order analysis to be run on a
multi-processor system.
The multi-processor code was calling the count_sobol_points() function of
the
specific_analyses.frame_order.optimisation module to give feedback when
calling the minimise.execute
or minimise.calculate user functions. However this was run in the slave
command run() method, hence
would be executed on the slave. The problem is that count_sobol_points()
performs a number of
checks on the current data pipe, however the slaves do not have any data
pipes set up.
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r27721 | bugman | 2015-02-25 14:16:04 +0100 (Wed, 25 Feb 2015) | 7 lines
Added the new 'atom_id' argument to the frame_order.distribute user
function.
This uses the new inverse selection functionality recently introduced into
the trunk to delete all
structural data not matching the atom_id from the copy of the loaded
structural data string prior to
generating the distribution of structures.
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r27806 | bugman | 2015-03-12 12:38:58 +0100 (Thu, 12 Mar 2015) | 12 lines
Bug fix for the frame order target function (introduced recently in r27715).
The copy.deepcopy() function is now used for all numpy input data to avoid
the data from being
modified between function calls. This is important for missing RDC and PCS
data which is sent in as
NaN values. In the target function __init__() method, the NaN values are
replaced by 0.0 after the
self.missing_rdc and self.missing_pcs structures have been by checking for
NaN values. However the
recent specific_analyses.frame_order.optimisation change in the
Frame_order_minimise_command slave
command to printout the number of integration points resulted in the target
function being
initialised twice, causing all NaN values to be 0.0 in the second
initialisation. Hence all missing
data was being treated as real data with values of 0.0.
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r27878 | bugman | 2015-09-25 14:30:22 +0200 (Fri, 25 Sep 2015) | 3 lines
Created a new skeleton chapter in the relax manual for the frame order
analysis.
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r27879 | bugman | 2015-09-25 15:10:04 +0200 (Fri, 25 Sep 2015) | 5 lines
Added a theory section to the new frame order chapter.
This is taken from an in-preparation supplement.
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r27880 | bugman | 2015-09-25 15:15:19 +0200 (Fri, 25 Sep 2015) | 6 lines
Rearrangement of the frame order chapter in the manual.
The theory section has been spun out into its own frame_order_theory.tex
LaTeX file for better
organisation.
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r27881 | bugman | 2015-09-25 15:26:00 +0200 (Fri, 25 Sep 2015) | 5 lines
Fix for the previous commit (r27880).
Most chapters had been commented out and accidentally committed.
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r27882 | bugman | 2015-09-25 20:15:46 +0200 (Fri, 25 Sep 2015) | 6 lines
Added two more sections to the frame order chapter of the manual.
This includes a frame order modelling section and PCS numerical integration
section. Both are from
a supplement from an in-preparation manuscript.
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r27883 | bugman | 2015-09-25 20:26:01 +0200 (Fri, 25 Sep 2015) | 3 lines
Added a DOI and ISBN number to the bibliography.
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r27884 | bugman | 2015-09-28 18:13:54 +0200 (Mon, 28 Sep 2015) | 3 lines
Moved the frame_order_theory.tex LaTeX file into the frame_order directory.
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r27885 | bugman | 2015-09-28 18:37:31 +0200 (Mon, 28 Sep 2015) | 3 lines
Shifted the frame order model derivations into their own 'Advanced topics'
chapter.
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r27886 | bugman | 2015-09-28 19:05:02 +0200 (Mon, 28 Sep 2015) | 3 lines
Cross-referencing fix.
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r27887 | bugman | 2015-09-29 13:51:04 +0200 (Tue, 29 Sep 2015) | 3 lines
Added the frame order sample scripts used in the CaM-IQ analysis.
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r27888 | bugman | 2015-09-29 16:02:20 +0200 (Tue, 29 Sep 2015) | 3 lines
Added an introduction for the frame order chapter of the manual.
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r27889 | bugman | 2015-09-29 16:15:49 +0200 (Tue, 29 Sep 2015) | 5 lines
Added a 'Data analysis' section to the frame order chapter of the manual.
This includes the N-state and frame order analysis scripts required to
perform a full analysis.
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r27890 | bugman | 2015-09-29 17:43:04 +0200 (Tue, 29 Sep 2015) | 6 lines
Editing of the data analysis section of the frame order chapter of the
manual.
A PCS structural error figure has been added, all the text improved, and
the scripts made to match
those in sample_scripts/frame_order/.
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r27891 | bugman | 2015-09-29 18:09:20 +0200 (Tue, 29 Sep 2015) | 3 lines
Added a section to the end of the frame order chapter about the long
computation times.
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r27892 | bugman | 2015-09-29 18:17:13 +0200 (Tue, 29 Sep 2015) | 5 lines
The 'scons clean' target now removes all LaTeX *.aux files.
The docs/latex/frame_order/ directory is now also being checked for *.aux
files.
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r27893 | bugman | 2015-09-29 18:17:47 +0200 (Tue, 29 Sep 2015) | 3 lines
Trailing whitespace removal in the full_analysis.py frame order sample
script.
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r27894 | bugman | 2015-09-29 18:23:52 +0200 (Tue, 29 Sep 2015) | 3 lines
Removed many unnecessary references to relax.
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r27895 | bugman | 2015-09-29 18:26:10 +0200 (Tue, 29 Sep 2015) | 3 lines
Removed lots of useless comments about book references.
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r27896 | bugman | 2015-09-29 18:43:07 +0200 (Tue, 29 Sep 2015) | 3 lines
Reference fix in the frame order chapter of the manual.
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r27897 | bugman | 2015-09-29 19:00:06 +0200 (Tue, 29 Sep 2015) | 3 lines
Added some images missing from the frame order chapter of the manual.
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r27898 | bugman | 2015-09-29 19:02:32 +0200 (Tue, 29 Sep 2015) | 3 lines
Avoided a doubly defined label in the manual.
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r27899 | bugman | 2015-09-29 19:06:50 +0200 (Tue, 29 Sep 2015) | 5 lines
Removed some duplicated text in the frame order models chapter of the
manual.
This is duplicated from the frame order analysis chapter.
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r27912 | bugman | 2015-10-01 14:59:38 +0200 (Thu, 01 Oct 2015) | 3 lines
Indentation fix for allowing the API documentation to be properly compiled.
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Added:
trunk/docs/latex/frame_order/
- copied from r27899,
branches/frame_order_cleanup/docs/latex/frame_order/
trunk/docs/latex/frame_order.tex
- copied unchanged from r27899,
branches/frame_order_cleanup/docs/latex/frame_order.tex
trunk/docs/latex/images/cam_iq_abc_whole_structural_noise.eps
- copied unchanged from r27899,
branches/frame_order_cleanup/docs/latex/images/cam_iq_abc_whole_structural_noise.eps
trunk/docs/latex/images/double_motion_system.eps.gz
- copied unchanged from r27899,
branches/frame_order_cleanup/docs/latex/images/double_motion_system.eps.gz
trunk/docs/latex/images/double_motion_system.svg
- copied unchanged from r27899,
branches/frame_order_cleanup/docs/latex/images/double_motion_system.svg
trunk/docs/latex/images/frame_order_matrix/
- copied from r27899,
branches/frame_order_cleanup/docs/latex/images/frame_order_matrix/
trunk/docs/latex/images/pec_diag.eps
- copied unchanged from r27899,
branches/frame_order_cleanup/docs/latex/images/pec_diag.eps
trunk/docs/latex/images/pec_y.eps
- copied unchanged from r27899,
branches/frame_order_cleanup/docs/latex/images/pec_y.eps
trunk/docs/latex/images/perm_iso_cone.eps.gz
- copied unchanged from r27899,
branches/frame_order_cleanup/docs/latex/images/perm_iso_cone.eps.gz
trunk/docs/latex/images/perm_pseudo_ellipse.eps.gz
- copied unchanged from r27899,
branches/frame_order_cleanup/docs/latex/images/perm_pseudo_ellipse.eps.gz
trunk/docs/latex/images/pseudo_elliptic_cone.eps
- copied unchanged from r27899,
branches/frame_order_cleanup/docs/latex/images/pseudo_elliptic_cone.eps
trunk/sample_scripts/frame_order/count_sobol_points.py
- copied unchanged from r27899,
branches/frame_order_cleanup/sample_scripts/frame_order/count_sobol_points.py
trunk/sample_scripts/frame_order/full_analysis.py
- copied unchanged from r27899,
branches/frame_order_cleanup/sample_scripts/frame_order/full_analysis.py
trunk/sample_scripts/frame_order/refinement.py
- copied unchanged from r27899,
branches/frame_order_cleanup/sample_scripts/frame_order/refinement.py
trunk/sample_scripts/frame_order/summarise.py
- copied unchanged
[... 64 lines stripped ...]
r27959 - in /trunk: ./ auto_analyses/ docs/latex/ docs/latex/frame_order/ docs/latex/images/ docs/latex/images/frame_order_m...