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Enable patchwise training and prediction #135

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131c434
stach changes
nilsleh Oct 10, 2023
3342b96
draft
nilsleh Oct 12, 2023
b7cf3fa
draft
nilsleh Oct 12, 2023
70f3783
merge main
nilsleh Oct 12, 2023
379e3b2
wrong merge
nilsleh Oct 12, 2023
85cd34b
incorporate some of the feedback
nilsleh Oct 13, 2023
be8fffd
run black
nilsleh Oct 13, 2023
3415377
merge main
nilsleh Nov 6, 2023
39dd15b
merge main
nilsleh Nov 6, 2023
876970e
layout code
nilsleh Apr 12, 2024
d1cb338
change __call__
nilsleh Apr 12, 2024
218f791
revert
nilsleh Apr 12, 2024
37fe771
type annotation
nilsleh Apr 12, 2024
fb20ccc
patch_size sampling test
nilsleh Apr 15, 2024
5bda80b
patchwise test trainer
nilsleh Apr 15, 2024
c276844
gridded window patching
Apr 19, 2024
fde7e02
adding sliding window patching function
Apr 19, 2024
195a923
loader with bboxes
nilsleh Apr 22, 2024
824df24
loader with boxes
nilsleh Apr 22, 2024
e6e1ae8
Altering kwargs to enable for-loop and change sliding function
Apr 22, 2024
e75d022
Merge branch 'patchwise_train' into msjr/patching
nilsleh Apr 22, 2024
bae0855
move logic to call
nilsleh Apr 22, 2024
a090d34
Merge branch 'main' into patchwise_train
nilsleh Apr 22, 2024
797f48e
Merge branch 'patchwise_train' into msjr/patching
nilsleh Apr 22, 2024
5291ec3
Merge pull request #1 from nilsleh/msjr/patching
nilsleh Apr 23, 2024
7b09119
typo
nilsleh Apr 23, 2024
282c2be
notebook with patchwise train
nilsleh Apr 24, 2024
dfa386d
refining stride to avoid error
Apr 24, 2024
8d46653
inference patching
Apr 27, 2024
acbad8b
predict_patches
Apr 28, 2024
3e2994e
patchwise predictions during inference and stitching
May 3, 2024
765849d
fix typo
May 3, 2024
abc9a9d
merge main
nilsleh Jun 11, 2024
7f8ef93
new cropped stitching
Jun 24, 2024
847a47c
clipped patchwise predictions, single date
Jun 26, 2024
f93fc39
correct minor errors/typos
Jun 27, 2024
07256f0
Merge pull request #2 from nilsleh/msjr-test_patching
nilsleh Jun 27, 2024
d8af314
use TODO to be uniform
davidwilby Jun 27, 2024
f3b7f12
use "stride" as in taskloader
davidwilby Jun 28, 2024
5a1766b
resolve unnormalised coordinate names
Jul 10, 2024
84d9944
Handle absent bbox and task as non-iterable
davidwilby Jul 11, 2024
aab6f1e
resolve unnormalised coordinate names
Jul 10, 2024
bda7176
use dict format for isel for variable coordinate names
davidwilby Jul 11, 2024
55bf86f
add basic test for patchwise prediction
davidwilby Jul 16, 2024
323ab46
handle patch_size and stride as floats or tuples in task loader and p…
davidwilby Jul 18, 2024
09befb3
test parameter handling and sizes in patchwise prediction
davidwilby Jul 19, 2024
c36455b
remove resolved TODO
davidwilby Jul 19, 2024
0cf143d
check patch_size and stride values in predict_patch and test
davidwilby Jul 19, 2024
8da48c1
test inference
nilsleh Aug 7, 2024
7cf556e
correct typo
Aug 8, 2024
ca6d001
resolve conflicts
Aug 8, 2024
bc862df
fix stride & patch checking
davidwilby Aug 9, 2024
61dc88e
revert previous commit
nilsleh Aug 9, 2024
f2bd5bb
fix patchwise training tests
davidwilby Aug 9, 2024
601102e
add actual training step to test_sliding_window_training
davidwilby Aug 9, 2024
64773fc
try to make printing work for task objects with bbox attribute
davidwilby Aug 9, 2024
69f0ac6
run black
davidwilby Aug 9, 2024
f5e4a8a
re-add missing code from task loader
davidwilby Aug 12, 2024
8aac7b6
Merge pull request #5 from nilsleh/dw/add_missing_loader_code
nilsleh Aug 12, 2024
c7a6172
Merge pull request #3 from nilsleh/msjr-test_patching
nilsleh Aug 12, 2024
5e29031
Commit to allow patching irrespective of whether x1 and x2 are ascend…
Aug 12, 2024
294cc47
changes to loader.py to ensure all patched tasks run left to right an…
Aug 12, 2024
4e136e3
Commit to make model agnostic to coord direction
Aug 13, 2024
6dd9b3a
Resolve conflicts primarily due to use of unnorm_name and orig_name
Aug 14, 2024
529e8c8
use more informative error message for predict_patch
davidwilby Aug 14, 2024
f37e28c
Merge branch 'patchwise_train' into dw/refactor_predict
davidwilby Aug 15, 2024
0344c2a
fix use of stride_size
davidwilby Aug 15, 2024
840838d
move patchwise parameter test to test_task_loader
davidwilby Aug 16, 2024
ceeb8ca
fix patch_size and stride for sliding window tests
davidwilby Aug 16, 2024
5fc1fe3
remove test as moved to test_task_loader
davidwilby Aug 16, 2024
1f434cc
check input parameters in task loader
davidwilby Aug 16, 2024
96edce8
For patchwise prediction, get patch_size and stride directly from task
davidwilby Aug 16, 2024
a705549
Merge pull request #6 from nilsleh/msjr-test_patching
nilsleh Aug 21, 2024
f5c015b
Merge branch 'patchwise_train' into dw/patch_size_from_task_for_predict
davidwilby Aug 21, 2024
c14d5d1
Merge pull request #7 from nilsleh/dw/patch_size_from_task_for_predict
nilsleh Aug 21, 2024
18f2e5a
raise errors instead of assert
davidwilby Aug 22, 2024
47d0998
use warning for stride > patch size
davidwilby Aug 22, 2024
df0533b
remove comment
davidwilby Aug 22, 2024
f7d57e9
raise error for stride > patch_size in prediction
davidwilby Aug 22, 2024
fed3940
alter paramaters for test
davidwilby Aug 22, 2024
b3a6dab
raise error for more than one date in predict_patch
davidwilby Aug 22, 2024
c8a38f2
black
davidwilby Aug 22, 2024
52a0cb3
Merge branch 'main' into dw/merge_main
davidwilby Aug 22, 2024
2672fec
Merge branch 'patchwise_train' into dw/refactor_predict
davidwilby Aug 22, 2024
e10d645
fix getting and checking of patch_size and stride
davidwilby Aug 22, 2024
f6f843d
fix docstrings and defaults
davidwilby Aug 22, 2024
2e5c6a8
reinstate orig_name patch clip slicing
davidwilby Aug 22, 2024
e4d5567
Merge pull request #8 from nilsleh/dw/merge_main
nilsleh Aug 22, 2024
e57f065
Merge branch 'patchwise_train' into dw/refactor_predict
davidwilby Aug 23, 2024
51d8c05
use hypothesis to expand on patchwise predict testing
davidwilby Aug 23, 2024
79afa12
Merge pull request #4 from nilsleh/dw/refactor_predict
davidwilby Aug 23, 2024
d6500f7
account for warnings/errors in patchwise task loader
davidwilby Aug 23, 2024
7c47357
allow longer test runs
davidwilby Aug 23, 2024
274902a
use patch size which relates to the normalised size
davidwilby Aug 23, 2024
60c7a14
alter docstring to reflect function
davidwilby Aug 23, 2024
cdbd73a
attempt fix for compute_x1x2_direction
davidwilby Aug 23, 2024
f1e3dfe
Merge branch 'dw/compute_coord_direction' into dw/fix_regression
davidwilby Aug 23, 2024
6f0e2e6
Merge pull request #5 from davidwilby/dw/fix_regression
davidwilby Sep 17, 2024
c0cd17e
address montonic and prediction size issues
Sep 17, 2024
d30e687
move patchwise test out of class
davidwilby Oct 11, 2024
7a100ee
Update deepsensor/model/model.py
MartinSJRogers Oct 15, 2024
23733df
Merge pull request #8 from davidwilby/montonic_errors
MartinSJRogers Oct 15, 2024
4a4276d
Move spatial slicing below gapfill sampling
Oct 31, 2024
2f0e2ba
Merge pull request #11 from davidwilby/gapfill_loop
MartinSJRogers Oct 31, 2024
e2488f3
Merge branch 'main' into patchwise_train
davidwilby Oct 31, 2024
54ee611
Merge remote-tracking branch 'origin/patchwise_train' into patchwise_…
davidwilby Oct 31, 2024
9b1f30d
lint patchwise code
davidwilby Oct 31, 2024
812e056
Update patchwise training notebook with additional descriptive text
Nov 1, 2024
3a34ed3
Merge pull request #13 from davidwilby/patchwise_linting
davidwilby Nov 5, 2024
4859f2d
rename notebook; use new tqdm notebook; other small tweaks to text
davidwilby Nov 5, 2024
53f238f
add correct output and prediction plot
davidwilby Nov 5, 2024
9e4254f
Merge branch 'patchwise_train' into update_notebook
davidwilby Nov 5, 2024
3e68ee1
Merge pull request #14 from davidwilby/update_notebook
davidwilby Nov 7, 2024
f7d5422
use python 3.8 compatible type hints
davidwilby Nov 13, 2024
527edff
rename predict_patch to predict_patchwise and fix references
davidwilby Nov 13, 2024
afac690
remove mention of contributing in error message
davidwilby Nov 13, 2024
277cdc3
refactor overlap calculation
davidwilby Nov 25, 2024
88ae024
use smaller test dataset
davidwilby Nov 25, 2024
325de6d
update docstring for predict_patchwise
davidwilby Nov 27, 2024
9d79b34
account for non-gridded data correctly
davidwilby Nov 29, 2024
4c05b77
refactor to reduce duplication; reduce floating point errors
davidwilby Nov 29, 2024
4b570ae
first attempt using merge
Nov 29, 2024
df88bc7
pass kwargs to predict; use data_processor attribute instead of arg
davidwilby Dec 2, 2024
4e028ab
correct typo
davidwilby Dec 2, 2024
657a42a
Replace combine by coords with method to infill blank prediction obje…
Dec 3, 2024
e68c01a
remove the +1 to prevent Nan lines forming
Dec 3, 2024
8b9a8ac
add some comments
davidwilby Dec 3, 2024
d620e88
Merge pull request #16 from davidwilby/refactor_sample_sliding
davidwilby Dec 3, 2024
3c1c1c8
Update deepsensor/model/model.py
MartinSJRogers Dec 3, 2024
e601109
linting
davidwilby Dec 13, 2024
a86ce31
tweak comments
davidwilby Dec 13, 2024
c7a994e
re-enable size checking in test
davidwilby Dec 13, 2024
e5b580b
rename some variables for slightly improved readability; add typehints
davidwilby Dec 20, 2024
91b83ce
Merge pull request #18 from davidwilby/replace_combineByCoords_with_m…
davidwilby Dec 20, 2024
158b6dc
Merge pull request #17 from davidwilby/predict_args
davidwilby Dec 20, 2024
747f7dd
reduce large comment block to easier to follow inline comments
davidwilby Jan 8, 2025
4f5eead
remove unused hypothesis dependency
davidwilby Jan 8, 2025
322766f
remove todo
davidwilby Jan 8, 2025
b4e9ff5
move coord direction calcuation to where it is needed
davidwilby Jan 9, 2025
572d7ec
clean up markup
Jan 9, 2025
da2f68f
Reduce repitiion and place code to determine coordinate extent in one…
Jan 10, 2025
c2f0ffe
Create DeepSensor object straight after stitching
Jan 10, 2025
9a7e743
Slightly amend some mark up text
Jan 10, 2025
e857355
Editted text for get_coordinate_extent_method
Jan 10, 2025
358b884
Edit where time is defined in stitched prediction object
Jan 10, 2025
58e9076
Reduce for loops and keep predictions as deepsensor.prediction objects
Jan 12, 2025
9943e99
Update deepsensor/model/model.py
MartinSJRogers Jan 21, 2025
53ee50f
Merge pull request #19 from davidwilby/simplify_stitching
davidwilby Jan 21, 2025
6cf0a28
Update deepsensor/model/model.py
MartinSJRogers Jan 22, 2025
1f0fb32
Merge pull request #20 from davidwilby/simplify_stitching_retain_pred…
davidwilby Jan 27, 2025
be883dc
lint
davidwilby Jan 27, 2025
b0459e8
use python 3.8 compatible typehint
davidwilby Jan 27, 2025
9765787
correct type hint
davidwilby Jan 27, 2025
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -11,3 +11,4 @@ dist/*
_build
*.png
deepsensor.egg-info/
.hypothesis/
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