Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Integrate Segway Toolkit into Segway #181

Open
wants to merge 95 commits into
base: develop
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
95 commits
Select commit Hold shift + click to select a range
05936cb
Change output to proper BED
isaiahah Jul 25, 2023
ef92989
Last file of BED format change
isaiahah Jul 25, 2023
c6c873c
Fix simpleseg test
isaiahah Jul 25, 2023
4356d20
Bugfix color assignment and posterior
isaiahah Jul 25, 2023
a4edc87
Fix data test
isaiahah Jul 25, 2023
29cc1b8
Fix multipledatasets test
isaiahah Jul 25, 2023
e6eafb1
Fix runroundinstance test
isaiahah Jul 25, 2023
eb5525e
Fix simpleconcat test
isaiahah Jul 25, 2023
5db5629
Fix simpleidentifysteps test
isaiahah Jul 26, 2023
7a60723
Fixed simplerecover test
isaiahah Jul 26, 2023
7b389b1
Fixed simpleresolution test
isaiahah Jul 26, 2023
178ac84
Fixed simplesemisupervised test
isaiahah Jul 26, 2023
eeffe89
Attempt to fix simplesubseg test
isaiahah Jul 26, 2023
431a578
Fixed simpletrainsteps test
isaiahah Jul 26, 2023
775301e
Fixed simplevirtualevidence test
isaiahah Jul 26, 2023
75b1b2c
Fix Pyflakes warnings
isaiahah Jul 26, 2023
e0878b9
Change to coloring by superlabel
isaiahah Jul 26, 2023
028f261
Bugfix extract_superlabel return type
isaiahah Jul 26, 2023
82914c7
Bugfix color assignment to superlabel
isaiahah Jul 26, 2023
70854a5
Begin addressing Eric's comments
isaiahah Jul 27, 2023
852886f
Remove unneeded import
isaiahah Jul 27, 2023
77fdf95
Begin responding to Eric's comments
isaiahah Jul 28, 2023
0cecaec
Complete posterior track output
isaiahah Jul 28, 2023
1cc687f
Fix data test
isaiahah Jul 28, 2023
478e321
Fix runroundinstance test
isaiahah Jul 28, 2023
a6707ee
Attempt to fix simplesubseg test
isaiahah Jul 28, 2023
bb3e7e1
Bugfix multi-item context manager for py<3.9
isaiahah Jul 28, 2023
87cc8c4
Cleanup comments and documentation
isaiahah Jul 28, 2023
035040e
Address Eric's comments
isaiahah Jul 31, 2023
d488be3
In progress GMTK API integration
isaiahah Sep 1, 2023
4138d48
Rename API files
isaiahah Oct 6, 2023
72b11f6
Merge Segway main into GMTK API
isaiahah Oct 6, 2023
354240a
flake8 fixes
isaiahah Oct 6, 2023
6b892aa
Merge branch 'master' of https://github.com/hoffmangroup/segway into …
isaiahah Oct 6, 2023
8c9afde
flake8 fixes
isaiahah Oct 6, 2023
0aff1e1
Convert Virtual Evidence to hard coded string
isaiahah Oct 7, 2023
0077e3b
Remove extra test files
isaiahah Oct 7, 2023
8908295
Draft GMTK API integration
isaiahah May 22, 2024
c7eea28
Bugfix DenseCPT DirichletTable implementation
isaiahah May 22, 2024
63615eb
Place format strings on one line
isaiahah May 22, 2024
eff60d6
Reorder sections to match template
isaiahah May 22, 2024
ebe17ea
Add conditional statement on INPUT_PARAMS_FILENAME
isaiahah May 23, 2024
7947649
Add clause to print condition on INPUT_PARAMS_FILENAME
isaiahah May 23, 2024
f3d9819
Use Segway toolkit as official input.master
isaiahah May 23, 2024
c7e3ab1
Fix segCountDown_seg_segTransition prob shape
isaiahah May 23, 2024
39a8f20
Print from-template input.master for testing
isaiahah May 23, 2024
6e61b11
Bugfix filename suffix
isaiahah May 23, 2024
39c3d58
Bugfix template input.master suffix
isaiahah May 23, 2024
f91348c
Undo previous bugfix
isaiahah May 23, 2024
dd7b63c
Attempt to debug segCountDown_seg_segTransition dimension
isaiahah May 23, 2024
edb2074
Remove support for Segway toolkit gamma distribution
isaiahah May 24, 2024
ec4ba8d
Bugfix removing Gamma distribution
isaiahah May 24, 2024
5035df7
Add preprocessor condition on VIRTUAL_EVIDENCE
isaiahah May 27, 2024
0ebf3a1
Add keep_shape for Dirichlet Table
isaiahah May 27, 2024
904cb42
Fix get_header_info for Dirichlet Tables
isaiahah May 27, 2024
3d47d64
Remove calls to InputMasterSaver class
isaiahah May 27, 2024
cfb36e0
Attempt to fix filename creation
isaiahah May 27, 2024
e5f5564
Hardcode input.master.tmpl resource name
isaiahah May 27, 2024
2520f26
Bugfix new file creation
isaiahah May 27, 2024
ae9d1ee
Bugfix filename assignment
isaiahah May 27, 2024
853531f
Add header and footers to sections for preprocessor conditions
isaiahah May 27, 2024
44d2255
Bugfix line_before
isaiahah May 27, 2024
00a419a
Add VirtualEvidence class
isaiahah May 27, 2024
380ed43
Fix type of VirtualEvidence section
isaiahah May 27, 2024
ff66b3e
Cleanup VirtualEvidence string
isaiahah May 27, 2024
f57ff1f
Minor code cleanup
isaiahah May 29, 2024
9b376e8
Move testing to generate input.master into save_input_master
isaiahah May 30, 2024
5889962
Re-add INPUT_MASTER_FILENAME
isaiahah May 30, 2024
b02316b
Fix exported filename
isaiahah May 30, 2024
d096ea2
Bugfix code change
isaiahah May 30, 2024
a038925
Attempt to bugfix input_master_filename
isaiahah May 30, 2024
97d75cf
Undo attempted changes from today
isaiahah May 30, 2024
f7f8e7b
Merge branch 'gmtk-api' of https://github.com/isaiahah/segway into gm…
isaiahah May 30, 2024
9c26a70
Revert changes from today
isaiahah May 30, 2024
f15876a
Remove old template system for input.master
isaiahah Jun 6, 2024
f9a5f31
Cleanup code checking if input.master exists
isaiahah Jun 6, 2024
f1a873e
Continue cleanup
isaiahah Jun 11, 2024
622f892
Additional code cleanup and flake8 fixes
isaiahah Jun 12, 2024
f3a1e52
input.master cleanup
isaiahah Jun 12, 2024
6c4245d
Rename segway_input_master
isaiahah Jun 13, 2024
3e960f4
Implement DirichletConst line in DPMF header
isaiahah Jun 13, 2024
e397c7f
Remove input.master.tmpl
isaiahah Jun 13, 2024
f4e28dc
flake8 fixes
isaiahah Jun 13, 2024
c3ed1ec
Add default preamble to support CNVway backward compatability
isaiahah Jun 13, 2024
20378f2
Load decision trees from data files
isaiahah Jun 14, 2024
679fe0a
Bugfix for Python3.9 (cannot check instance with generic)
isaiahah Jun 14, 2024
a087573
Address Eric's comments
isaiahah Jun 24, 2024
8c9703b
Remove RealMat class
isaiahah Jul 2, 2024
df8c2db
Address Eric's comments
isaiahah Jul 5, 2024
62917f9
Update OBJ_KIND for Generic String
isaiahah Jul 8, 2024
72a38f8
Remove references to ArbitraryString
isaiahah Jul 10, 2024
6a6e60b
flake8 fixes
isaiahah Jul 10, 2024
b1bef31
Rename toolkit file to params.py
isaiahah Jul 12, 2024
74ebfe1
Address Michael's comments
isaiahah Aug 30, 2024
072d3e8
Call make_cardinality_line more
isaiahah Aug 30, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
74 changes: 0 additions & 74 deletions segway/data/input.master.tmpl

This file was deleted.

1 change: 0 additions & 1 deletion segway/data/map_frameIndex_ruler.dt.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
map_frameIndex_ruler
1
% is the frameIndex divisible by RULER_SCALE
-1 { mod(p0, RULER_SCALE) == 0 }
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
map_segTransition_ruler_seg_segCountDown_segCountDown
4
0 2 2 default
% segTransition(0) == 2 (seg transition):
Expand Down
1 change: 0 additions & 1 deletion segway/data/map_seg_segCountDown.dt.tmpl
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
map_seg_segCountDown
1
% this is only used at the beginning of an observation track
0 $tree
3 changes: 0 additions & 3 deletions segway/data/map_seg_subseg_obs.dt.txt
Original file line number Diff line number Diff line change
@@ -1,5 +1,2 @@
% XXXopt: good candidate for a linear combination C deterministic mapper

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Can you please restore this comment?

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Actually, it might be better to move it to whatever Python code calls this so it isn't copied into every project.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I've moved this comment (verbatim) to the Python code which loads this file. See input_master.py line 121.

map_seg_subseg_obs
2 % num parents
-1 { p0*CARD_SUBSEG + p1 }
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
map_supervisionLabel_seg_alwaysTrue
2 % num parents
% first parent is the label: 0 = no label; 1+ = (desired-1)
% second parent is target
Expand Down
5 changes: 5 additions & 0 deletions segway/data/preamble.tmpl
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
#include "$include_file"

#if CARD_SEG != $card_seg
#error Specified number of segment labels (CARD_SEG) does not match the number used for this input master file ($card_seg)
#endif
Loading
Loading