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schema: '2.0'
stages:
createtiles@2019:
cmd: mkdir -p data/processed.images.2019; gdal_retile.py -csv locations.csv -v
-ps 2048 2048 -co "TILED=YES" -co "COMPRESS=LZW" -co "PREDICTOR=2" -co "ALPHA=NO"
-co "NUM_THREADS=ALL_CPUS" -targetDir data/processed.images.2019 data/raw/ortho_ms_2019_EPSG3044.tif
deps:
- path: data/raw/ortho_ms_2019_EPSG3044.tif
md5: 28a27ea53b559c3cec937a3687407557
size: 144920418531
params:
params.yaml:
source_dim: 2048
outs:
- path: data/processed.images.2019
md5: 35c31b781cb0bdb19650329132d83d05.dir
size: 144926802415
nfiles: 30489
createmasks:
cmd: python scripts/createmasks.py data/processed.images.2019 data/processed.masks.2019 data/raw/shapefiles/deadtrees_2019/deadtrees_2019.shp
--negativesample data/raw/shapefiles/deadtrees_notdead/deadtrees_notdead.shp
deps:
- path: data/processed.images.2019
md5: 35c31b781cb0bdb19650329132d83d05.dir
size: 144926802415
nfiles: 30489
- path: data/raw/shapefiles/deadtrees_2019
md5: 206432f450611c44ceb32c49e50aa8c9.dir
size: 3996517
nfiles: 5
- path: data/raw/shapefiles/deadtrees_notdead
md5: 99b6d382aebfc46e79c9d044e95add4e.dir
size: 31722
nfiles: 5
outs:
- path: data/processed.masks.2019
md5: 86dfe9fff1765527e6ab7bdbd50e873d.dir
size: 4103103156
nfiles: 978
- path: data/processed.masks.2019.neg_sample
md5: e39614f069603f65a333d0a8713072a9.dir
size: 335615520
nfiles: 80
createdataset:
cmd: python scripts/createdataset.py data/processed.images.2019 data/processed.masks.2019 data/dataset --source_dim
2048 --tile_size 256 --format TIFF
deps:
- path: data/processed.images.2019
md5: 35c31b781cb0bdb19650329132d83d05.dir
size: 144926802415
nfiles: 30489
- path: data/processed.masks.2019
md5: 86dfe9fff1765527e6ab7bdbd50e873d.dir
size: 4103103156
nfiles: 978
- path: data/processed.masks.2019.neg_sample
md5: e39614f069603f65a333d0a8713072a9.dir
size: 335615520
nfiles: 80
params:
params.yaml:
createdataset.tile_size: 256
file_type: TIFF
source_dim: 2048
outs:
- path: data/dataset/stats.csv
md5: 5d5e6ab2648bdb6b7846d4c8655a72a8
size: 2539255
- path: data/dataset/train
md5: 09daf34f435e8a47ce8879a6f7a9899e.dir
size: 10832783360
nfiles: 208
createbalanced:
cmd: python scripts/createbalanced.py data/dataset/stats.csv data/dataset/train data/dataset/train_balanced data/dataset/train_balanced_short
--format TIFF --tmp-dir ./tmp
deps:
- path: data/dataset/stats.csv
md5: 8f24c9c9fcbcab4f9388a4b2b26ed58c
size: 2415683
- path: data/dataset/train
md5: a5a9bd6897f3c8b0143e3a378928cc54.dir
size: 20627302400
nfiles: 121
params:
params.yaml:
file_type: TIFF
outs:
- path: data/dataset/train_balanced
md5: 00c0e3636b55b92b63add488a2e62a12.dir
size: 20596592640
nfiles: 241
- path: data/dataset/train_balanced_short
md5: 94e764aa3326c386524910bfbac0454d.dir
size: 2072975360
nfiles: 97
createtiles@2017:
cmd: mkdir -p data/processed.images.2017; gdal_retile.py -csv locations.csv -v
-ps 2048 2048 -co "TILED=YES" -co "COMPRESS=LZW" -co "PREDICTOR=2" -co "ALPHA=NO"
-co "NUM_THREADS=ALL_CPUS" -targetDir data/processed.images.2017 data/raw/ortho_ms_2017_EPSG3044.tif
deps:
- path: data/raw/ortho_ms_2017_EPSG3044.tif
md5: 2389bdb4952d2c869c52e87abce30d4f
size: 109896357004
params:
params.yaml:
source_dim: 2048
outs:
- path: data/processed.images.2017
md5: 66de96d201af5a47a09997691b992370.dir
size: 109902740888
nfiles: 30489
inference@2017:
cmd: mkdir -p data/predicted.2017; stdbuf -i0 -o0 -e0 python scripts/inference.py
--all --nopreview -o data/predicted.2017 data/processed.images.2017; gdal_merge.py -co
"TILED=YES" -co "COMPRESS=LZW" -co "PREDICTOR=2" -co "NUM_THREADS=ALL_CPUS"
-o data/predicted_mosaic_2017.tif data/predicted.2017/ortho_ms_2017_EPSG3044_*
deps:
- path: checkpoints/bestmodel.ckpt
md5: fa7e507a107381e5dd9c2ebc9ddef09f
size: 378649412
- path: data/processed.images.2017
md5: 66de96d201af5a47a09997691b992370.dir
size: 109902740888
nfiles: 30489
outs:
- path: data/predicted.2017
md5: 6991e5e7cf8144ff46445ef25214fce6.dir
size: 601515230
nfiles: 20827
- path: data/predicted_mosaic_2017.tif
md5: 7cef75e791ea66524e8afdac1419e7e5
size: 839252195
inference@2019:
cmd: mkdir -p data/predicted.2019; stdbuf -i0 -o0 -e0 python scripts/inference.py
--all --nopreview -o data/predicted.2019 data/processed.images.2019; gdal_merge.py -co
"TILED=YES" -co "COMPRESS=LZW" -co "PREDICTOR=2" -co "NUM_THREADS=ALL_CPUS"
-o data/predicted_mosaic_2019.tif data/predicted.2019/ortho_ms_2019_EPSG3044_*
deps:
- path: checkpoints/bestmodel.ckpt
md5: fa7e507a107381e5dd9c2ebc9ddef09f
size: 378649412
- path: data/processed.images.2019
md5: 35c31b781cb0bdb19650329132d83d05.dir
size: 144926802415
nfiles: 30489
outs:
- path: data/predicted.2019
md5: 88d9fe4afe7054d15e5014b9743d87c9.dir
size: 484982007
nfiles: 16227
- path: data/predicted_mosaic_2019.tif
md5: fd472cc45d61c7223cbd09ab2872a30a
size: 811774816
computestats:
cmd: 'python scripts/computestats.py --frac 0.1 data/processed.images.2017 data/processed.images.2018 data/processed.images.2019 data/processed.images.2020 '
deps:
- path: data/processed.images.2017
md5: 66de96d201af5a47a09997691b992370.dir
size: 109902740888
nfiles: 30489
- path: data/processed.images.2018
md5: cfa0adee6401f838f162a0510085becf.dir
size: 144861203951
nfiles: 30489
- path: data/processed.images.2019
md5: 35c31b781cb0bdb19650329132d83d05.dir
size: 144926802415
nfiles: 30489
- path: data/processed.images.2020
md5: 76d4daf0d9e69904a9370a0c74006d17.dir
size: 163333629599
nfiles: 30489
outs:
- path: data/processed.images.stats.json
md5: 1ed04cbf29c00ed439bfa15bc170c5cb
computestatsinference:
cmd: 'python scripts/computestats_inference.py data/predicted.2017 data/predicted.2018 data/predicted.2019 data/predicted.2020 '
deps:
- path: data/predicted.2017
md5: 6991e5e7cf8144ff46445ef25214fce6.dir
size: 601515230
nfiles: 20827
- path: data/predicted.2018
md5: 6dc4d6140a683a68243cd01d5d733001.dir
size: 551422735
nfiles: 19182
- path: data/predicted.2019
md5: 88d9fe4afe7054d15e5014b9743d87c9.dir
size: 484982007
nfiles: 16227
- path: data/predicted.2020
md5: ca8bf8b4c611989f5c962b07dee85344.dir
size: 489635809
nfiles: 16125
outs:
- path: data/predicted.stats.csv
md5: 1b921ebb714f7234afd0d8b63f59a8d7
size: 1916604
createtiles@2018:
cmd: mkdir -p data/processed.images.2018; gdal_retile.py -csv locations.csv -v
-ps 2048 2048 -co "TILED=YES" -co "COMPRESS=LZW" -co "PREDICTOR=2" -co "ALPHA=NO"
-co "NUM_THREADS=ALL_CPUS" -targetDir data/processed.images.2018 data/raw/ortho_ms_2018_EPSG3044.tif
deps:
- path: data/raw/ortho_ms_2018_EPSG3044.tif
md5: 59fc13ae47105e690ecc396202c2bc30
size: 144854820067
params:
params.yaml:
source_dim: 2048
outs:
- path: data/processed.images.2018
md5: cfa0adee6401f838f162a0510085becf.dir
size: 144861203951
nfiles: 30489
createtiles@2020:
cmd: mkdir -p data/processed.images.2020; gdal_retile.py -csv locations.csv -v
-ps 2048 2048 -co "TILED=YES" -co "COMPRESS=LZW" -co "PREDICTOR=2" -co "ALPHA=NO"
-co "NUM_THREADS=ALL_CPUS" -targetDir data/processed.images.2020 data/raw/ortho_ms_2020_EPSG3044.tif
deps:
- path: data/raw/ortho_ms_2020_EPSG3044.tif
md5: 0ecdb70decb68b2d37446b21977d09f9
size: 163327245715
params:
params.yaml:
source_dim: 2048
outs:
- path: data/processed.images.2020
md5: 76d4daf0d9e69904a9370a0c74006d17.dir
size: 163333629599
nfiles: 30489
inference@2018:
cmd: mkdir -p data/predicted.2018; stdbuf -i0 -o0 -e0 python scripts/inference.py
--all --nopreview -o data/predicted.2018 data/processed.images.2018; gdal_merge.py -co
"TILED=YES" -co "COMPRESS=LZW" -co "PREDICTOR=2" -co "NUM_THREADS=ALL_CPUS"
-o data/predicted_mosaic_2018.tif data/predicted.2018/ortho_ms_2018_EPSG3044_*
deps:
- path: checkpoints/bestmodel.ckpt
md5: fa7e507a107381e5dd9c2ebc9ddef09f
size: 378649412
- path: data/processed.images.2018
md5: cfa0adee6401f838f162a0510085becf.dir
size: 144861203951
nfiles: 30489
outs:
- path: data/predicted.2018
md5: 6dc4d6140a683a68243cd01d5d733001.dir
size: 551422735
nfiles: 19182
- path: data/predicted_mosaic_2018.tif
md5: f8ae9346bf27514a30592e745ab87bc1
size: 830985617
inference@2020:
cmd: mkdir -p data/predicted.2020; stdbuf -i0 -o0 -e0 python scripts/inference.py
--all --nopreview -o data/predicted.2020 data/processed.images.2020; gdal_merge.py -co
"TILED=YES" -co "COMPRESS=LZW" -co "PREDICTOR=2" -co "NUM_THREADS=ALL_CPUS"
-o data/predicted_mosaic_2020.tif data/predicted.2020/ortho_ms_2020_EPSG3044_*
deps:
- path: checkpoints/bestmodel.ckpt
md5: fa7e507a107381e5dd9c2ebc9ddef09f
size: 378649412
- path: data/processed.images.2020
md5: 76d4daf0d9e69904a9370a0c74006d17.dir
size: 163333629599
nfiles: 30489
outs:
- path: data/predicted.2020
md5: ca8bf8b4c611989f5c962b07dee85344.dir
size: 489635809
nfiles: 16125
- path: data/predicted_mosaic_2020.tif
md5: 5e3c82736e20844bb9b1fc6f4d6cbbb6
size: 812671767
createmasks@2017:
cmd: python scripts/createmasks.py data/processed.images.2017 data/processed.masks.2017 data/raw/shapefiles/deadtrees_2017/deadtrees_2017.shp
deps:
- path: data/processed.images.2017
md5: 66de96d201af5a47a09997691b992370.dir
size: 109902740888
nfiles: 30489
- path: data/raw/shapefiles/deadtrees_2017
md5: 8d9432d5827254797ae04f89ec30aae1.dir
size: 811993
nfiles: 6
outs:
- path: data/processed.masks.2017
md5: ed46f628af2e934ce245fef7bb707d02.dir
size: 3633218132
nfiles: 866
createdataset@2017:
cmd: python scripts/createdataset.py data/processed.images.2017 data/processed.masks.2017 data/processed.lus.2017 data/dataset --subdir
train_2017 --source_dim 2048 --tile_size 256 --format TIFF --stats stats_2017.csv
deps:
- path: data/processed.images.2017
md5: 66de96d201af5a47a09997691b992370.dir
size: 109902740888
nfiles: 30489
- path: data/processed.lus.2017
md5: cd93e1d1eb4f857a9dab0cdc9e61c476.dir
size: 54193516092
nfiles: 12918
- path: data/processed.masks.2017
md5: ed46f628af2e934ce245fef7bb707d02.dir
size: 3633218132
nfiles: 866
params:
params.yaml:
createdataset.tile_size: 256
file_type: TIFF
source_dim: 2048
outs:
- path: data/dataset/stats_2017.csv
md5: b29cb5609b2c95ab0e819619279d4c1c
size: 2258658
- path: data/dataset/train_2017
md5: 325e1c100e27b7ba458f7a49ad45b311.dir
size: 738652160
nfiles: 29
createdataset@2019:
cmd: python scripts/createdataset.py data/processed.images.2019 data/processed.masks.2019 data/processed.lus.2019 data/dataset --subdir
train_2019 --source_dim 2048 --tile_size 256 --format TIFF --stats stats_2019.csv
deps:
- path: data/processed.images.2019
md5: 35c31b781cb0bdb19650329132d83d05.dir
size: 144926802415
nfiles: 30489
- path: data/processed.lus.2019
md5: e7700c6cafd6d3140afc916637ef54c6.dir
size: 54193516092
nfiles: 12918
- path: data/processed.masks.2019
md5: 83ce7ca88e1ed7fbf401d0d185ec261d.dir
size: 4103103156
nfiles: 978
params:
params.yaml:
createdataset.tile_size: 256
file_type: TIFF
source_dim: 2048
outs:
- path: data/dataset/stats_2019.csv
md5: c4bdc60a6b48ccbf31bba9c7504c19fe
size: 2513851
- path: data/dataset/train_2019
md5: c39665bff457346b2537a4a3a511b50b.dir
size: 1519052800
nfiles: 60
createmasks@2019:
cmd: python scripts/createmasks.py data/processed.images.2019 data/processed.masks.2019 data/raw/shapefiles/deadtrees_2019/deadtrees_2019.shp
deps:
- path: data/processed.images.2019
md5: 35c31b781cb0bdb19650329132d83d05.dir
size: 144926802415
nfiles: 30489
- path: data/raw/shapefiles/deadtrees_2019
md5: 206432f450611c44ceb32c49e50aa8c9.dir
size: 3996517
nfiles: 5
outs:
- path: data/processed.masks.2019
md5: 83ce7ca88e1ed7fbf401d0d185ec261d.dir
size: 4103103156
nfiles: 978
mergedatasets:
cmd: python scripts/mergedatasets.py data/dataset/train_2017 data/dataset/train_2019
deps:
- path: data/dataset/train_2017
md5: 325e1c100e27b7ba458f7a49ad45b311.dir
size: 738652160
nfiles: 29
- path: data/dataset/train_2019
md5: c39665bff457346b2537a4a3a511b50b.dir
size: 1519052800
nfiles: 60
outs:
- path: data/dataset/test
md5: 3ed97313db477e2d5f59e46b3d217014.dir
size: 202332160
nfiles: 9
- path: data/dataset/train
md5: 741a1c98ab0e5dcf2f896dde2ff6f5a8.dir
size: 1592913920
nfiles: 62
- path: data/dataset/val
md5: 14cbc9d627fef88c676cfbee18530b3f.dir
size: 462458880
nfiles: 18
createforestmasks@2019:
cmd: python scripts/createmasks.py data/processed.images.2019 data/processed.lus.2019 data/raw/shapefiles/forestmask/CORINE_forest.shp
--simple
deps:
- path: data/processed.images.2019
md5: 35c31b781cb0bdb19650329132d83d05.dir
size: 144926802415
nfiles: 30489
- path: data/raw/shapefiles/forestmask/CORINE_forest.shp
md5: 63947721b118c62a091559483db5d8f6
size: 43334576
outs:
- path: data/processed.lus.2019
md5: e7700c6cafd6d3140afc916637ef54c6.dir
size: 54193516092
nfiles: 12918
createforestmasks@2017:
cmd: python scripts/createmasks.py data/processed.images.2017 data/processed.lus.2017 data/raw/shapefiles/forestmask/CORINE_forest.shp
--simple
deps:
- path: data/processed.images.2017
md5: 66de96d201af5a47a09997691b992370.dir
size: 109902740888
nfiles: 30489
- path: data/raw/shapefiles/forestmask/CORINE_forest.shp
md5: 63947721b118c62a091559483db5d8f6
size: 43334576
outs:
- path: data/processed.lus.2017
md5: cd93e1d1eb4f857a9dab0cdc9e61c476.dir
size: 54193516092
nfiles: 12918
createmasks@2020:
cmd: python scripts/createmasks.py data/processed.images.2020 data/processed.masks.2020 data/raw/shapefiles/deadtrees_2020_test/deadtrees_2020_test.shp
deps:
- path: data/processed.images.2020
md5: 76d4daf0d9e69904a9370a0c74006d17.dir
size: 163333629599
nfiles: 30489
- path: data/raw/shapefiles/deadtrees_2020_test
md5: 2a046c036168c2c799ec3e7ff2ac4bc4.dir
size: 747779
nfiles: 5
outs:
- path: data/processed.masks.2020
md5: 64ab160672cf600aafc0292164150af2.dir
size: 247528718
nfiles: 59
createmasks@2018:
cmd: python scripts/createmasks.py data/processed.images.2018 data/processed.masks.2018 data/raw/shapefiles/deadtrees_2018_test/deadtrees_2018_test.shp
deps:
- path: data/processed.images.2018
md5: cfa0adee6401f838f162a0510085becf.dir
size: 144861203951
nfiles: 30489
- path: data/raw/shapefiles/deadtrees_2018_test
md5: d0f0aad50514c79c8939acc9c29683bf.dir
size: 65551
nfiles: 5
outs:
- path: data/processed.masks.2018
md5: df9b55bc5bfd32cfedaafe633d4963ec.dir
size: 121666658
nfiles: 29
createforestmasks@2018:
cmd: python scripts/createmasks.py data/processed.images.2018 data/processed.lus.2018 data/raw/shapefiles/forestmask/CORINE_forest.shp
--simple
deps:
- path: data/processed.images.2018
md5: cfa0adee6401f838f162a0510085becf.dir
size: 144861203951
nfiles: 30489
- path: data/raw/shapefiles/forestmask/CORINE_forest.shp
md5: 63947721b118c62a091559483db5d8f6
size: 43334576
outs:
- path: data/processed.lus.2018
md5: 692742b22e690cfbbef15101c24078c5.dir
size: 54193516092
nfiles: 12918
createforestmasks@2020:
cmd: python scripts/createmasks.py data/processed.images.2020 data/processed.lus.2020 data/raw/shapefiles/forestmask/CORINE_forest.shp
--simple
deps:
- path: data/processed.images.2020
md5: 76d4daf0d9e69904a9370a0c74006d17.dir
size: 163333629599
nfiles: 30489
- path: data/raw/shapefiles/forestmask/CORINE_forest.shp
md5: 63947721b118c62a091559483db5d8f6
size: 43334576
outs:
- path: data/processed.lus.2020
md5: 10691c48713cdf6555842329a31cf9a2.dir
size: 54193516092
nfiles: 12918
createdataset@2018:
cmd: python scripts/createdataset.py data/processed.images.2018 data/processed.masks.2018 data/processed.lus.2018 data/dataset --subdir
train_2018 --source_dim 2048 --tile_size 256 --format TIFF --stats stats_2018.csv
deps:
- path: data/processed.images.2018
md5: cfa0adee6401f838f162a0510085becf.dir
size: 144861203951
nfiles: 30489
- path: data/processed.lus.2018
md5: 692742b22e690cfbbef15101c24078c5.dir
size: 54193516092
nfiles: 12918
- path: data/processed.masks.2018
md5: df9b55bc5bfd32cfedaafe633d4963ec.dir
size: 121666658
nfiles: 29
params:
params.yaml:
createdataset.tile_size: 256
file_type: TIFF
source_dim: 2048
outs:
- path: data/dataset/stats_2018.csv
md5: aea5a89c55e0f0b3ab2a1c1bbccf218d
size: 76225
- path: data/dataset/train_2018
md5: 5a70790f4dc3df08571e3994c5421205.dir
size: 25692160
nfiles: 1
createdataset@2020:
cmd: python scripts/createdataset.py data/processed.images.2020 data/processed.masks.2020 data/processed.lus.2020 data/dataset --subdir
train_2020 --source_dim 2048 --tile_size 256 --format TIFF --stats stats_2020.csv
deps:
- path: data/processed.images.2020
md5: 76d4daf0d9e69904a9370a0c74006d17.dir
size: 163333629599
nfiles: 30489
- path: data/processed.lus.2020
md5: 10691c48713cdf6555842329a31cf9a2.dir
size: 54193516092
nfiles: 12918
- path: data/processed.masks.2020
md5: 64ab160672cf600aafc0292164150af2.dir
size: 247528718
nfiles: 59
params:
params.yaml:
createdataset.tile_size: 256
file_type: TIFF
source_dim: 2048
outs:
- path: data/dataset/stats_2020.csv
md5: fbeccb80c0c127aafd2a3009d8a1cf1a
size: 148564
- path: data/dataset/train_2020
md5: a7ef5b8149ea1b419ab2d22ad60165e5.dir
size: 146124800
nfiles: 6