diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 271b1daf7274419b0577a9dc37a862c8b3eab5ab..7e7f213e8fc2792a60cb1cbf6e45b0bac49190ed 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -3,6 +3,9 @@ image: gitlab-registry.irstea.fr/remi.cresson/otbtf:2.4-cpu-basic-testing
variables:
OTB_BUILD: /src/otb/build/OTB/build # Local OTB build directory
OTBTF_SRC: /src/otbtf # Local OTBTF source directory
+ OTB_TEST_DIR: $OTB_BUILD/Testing/Temporary # OTB testing directory
+ ARTIFACT_TEST_DIR: $CI_PROJECT_DIR/testing
+ CRC_BOOK_TMP: /tmp/crc_book_tests_tmp
workflow:
rules:
@@ -13,13 +16,17 @@ stages:
- Build
- Static Analysis
- Test
+ - Applications Test
.update_otbtf_src: &update_otbtf_src
- sudo rm -rf $OTBTF_SRC && sudo ln -s $PWD $OTBTF_SRC # Replace local OTBTF source directory
.compile_otbtf: &compile_otbtf
- cd $OTB_BUILD && sudo make install -j$(nproc --all) # Rebuild OTB with new OTBTF sources
-
+
+.install_pytest: &install_pytest
+ - pip3 install pytest pytest-cov pytest-order # Install pytest stuff
+
before_script:
- *update_otbtf_src
@@ -60,21 +67,47 @@ ctest:
stage: Test
script:
- *compile_otbtf
- - sudo rm -rf $OTB_BUILD/Testing/Temporary/* # Empty testing temporary folder (old files here)
+ - sudo rm -rf $OTB_TEST_DIR/* # Empty testing temporary folder (old files here)
- cd $OTB_BUILD/ && sudo ctest -L OTBTensorflow # Run ctest
after_script:
- - cp -r $OTB_BUILD/Testing/Temporary $CI_PROJECT_DIR/testing # Copy artifacts (they must be in $CI_PROJECT_DIR)
+ - cp -r $OTB_TEST_DIR $ARTIFACT_TEST_DIR
artifacts:
paths:
- - testing/*.*
+ - $ARTIFACT_TEST_DIR/*.*
expire_in: 1 week
when: on_failure
+.applications_test_base:
+ stage: Applications Test
+ rules:
+ # Only for MR targeting 'develop' branch because applications tests are slow
+ - if: $CI_MERGE_REQUEST_ID && $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == 'develop'
+ artifacts:
+ when: on_failure
+ paths:
+ - $CI_PROJECT_DIR/report_*.xml
+ - $ARTIFACT_TEST_DIR/*.*
+ expire_in: 1 week
+
+crc_book:
+ extends: .applications_test_base
+ script:
+ - *compile_otbtf
+ - *install_pytest
+ - cd $CI_PROJECT_DIR
+ - mkdir -p $CRC_BOOK_TMP
+ - TMPDIR=$CRC_BOOK_TMP \
+ DATADIR=$CI_PROJECT_DIR/test/data \
+ python -m pytest --junitxml=$CI_PROJECT_DIR/report_tutorial.xml $OTBTF_SRC/test/tutorial_unittest.py
+ after_script:
+ - mkdir -p $ARTIFACT_TEST_DIR
+ - cp $CRC_BOOK_TMP/*.* $ARTIFACT_TEST_DIR/
+
sr4rs:
- stage: Test
+ extends: .applications_test_base
script:
- *compile_otbtf
- - pip3 install pytest pytest-cov
+ - *install_pytest
- cd $CI_PROJECT_DIR
- wget -O sr4rs_sentinel2_bands4328_france2020_savedmodel.zip
https://nextcloud.inrae.fr/s/boabW9yCjdpLPGX/download/sr4rs_sentinel2_bands4328_france2020_savedmodel.zip
@@ -85,8 +118,4 @@ sr4rs:
- git clone https://github.com/remicres/sr4rs.git
- export PYTHONPATH=$PYTHONPATH:$PWD/sr4rs
- python -m pytest --junitxml=$CI_PROJECT_DIR/report_sr4rs.xml $OTBTF_SRC/test/sr4rs_unittest.py
- artifacts:
- when: on_failure
- paths:
- - $CI_PROJECT_DIR/report_sr4rs.xml
- expire_in: 1 week
+
diff --git a/test/data/RF_model_from_deep_features_map.tif b/test/data/RF_model_from_deep_features_map.tif
new file mode 100644
index 0000000000000000000000000000000000000000..d41d832c4d1e4f9848636d76f45cac26a1fdce15
Binary files /dev/null and b/test/data/RF_model_from_deep_features_map.tif differ
diff --git a/test/data/amsterdam_labels_A.tif b/test/data/amsterdam_labels_A.tif
new file mode 100644
index 0000000000000000000000000000000000000000..d07a0e0cfbcfad1f6b1b887ddf2a9470687c58be
Binary files /dev/null and b/test/data/amsterdam_labels_A.tif differ
diff --git a/test/data/amsterdam_labels_B.tif b/test/data/amsterdam_labels_B.tif
new file mode 100644
index 0000000000000000000000000000000000000000..b7af54a4c573aa9bbf1c7407e7dac9597a5a19e2
Binary files /dev/null and b/test/data/amsterdam_labels_B.tif differ
diff --git a/test/data/amsterdam_patches_A.tif b/test/data/amsterdam_patches_A.tif
new file mode 100644
index 0000000000000000000000000000000000000000..e8d2e70ece62fd8c1e20820b74c0edf2f16f80dd
Binary files /dev/null and b/test/data/amsterdam_patches_A.tif differ
diff --git a/test/data/amsterdam_patches_B.tif b/test/data/amsterdam_patches_B.tif
new file mode 100644
index 0000000000000000000000000000000000000000..d6b20fc81a85a57f09af319aa74af7e5e7cf76dc
Binary files /dev/null and b/test/data/amsterdam_patches_B.tif differ
diff --git a/test/data/classif_model1.tif b/test/data/classif_model1.tif
new file mode 100644
index 0000000000000000000000000000000000000000..a681cfd6a22867778b5b5452ab881f0352d567ba
Binary files /dev/null and b/test/data/classif_model1.tif differ
diff --git a/test/data/classif_model2.tif b/test/data/classif_model2.tif
new file mode 100644
index 0000000000000000000000000000000000000000..9b23ede1e26a72a52c843038f56b7b762e4f0d1b
Binary files /dev/null and b/test/data/classif_model2.tif differ
diff --git a/test/data/classif_model3_fcn.tif b/test/data/classif_model3_fcn.tif
new file mode 100644
index 0000000000000000000000000000000000000000..8109d0d7432b321055c9562d613710603dbd4b99
Binary files /dev/null and b/test/data/classif_model3_fcn.tif differ
diff --git a/test/data/classif_model3_pb.tif b/test/data/classif_model3_pb.tif
new file mode 100644
index 0000000000000000000000000000000000000000..028c5cefaf60344b80aeafe7c6bc03b19034f206
Binary files /dev/null and b/test/data/classif_model3_pb.tif differ
diff --git a/test/data/classif_model4.tif b/test/data/classif_model4.tif
new file mode 100644
index 0000000000000000000000000000000000000000..b87fe1e3f61613301b2d496fdd0ff41e5c66da53
Binary files /dev/null and b/test/data/classif_model4.tif differ
diff --git a/test/data/fake_spot6.jp2 b/test/data/fake_spot6.jp2
new file mode 100644
index 0000000000000000000000000000000000000000..6464ca60b7a86fc18b0be664885466ab064c6262
Binary files /dev/null and b/test/data/fake_spot6.jp2 differ
diff --git a/test/data/outvec_A.gpkg b/test/data/outvec_A.gpkg
new file mode 100644
index 0000000000000000000000000000000000000000..87c8301d562985ceb5bc97f0c899cfd4c07de294
Binary files /dev/null and b/test/data/outvec_A.gpkg differ
diff --git a/test/data/outvec_B.gpkg b/test/data/outvec_B.gpkg
new file mode 100644
index 0000000000000000000000000000000000000000..78578a3a204cb393478905492dd8b859aaa5691e
Binary files /dev/null and b/test/data/outvec_B.gpkg differ
diff --git a/test/data/s2_10m_labels_A.tif b/test/data/s2_10m_labels_A.tif
new file mode 100644
index 0000000000000000000000000000000000000000..1af82324acce9247ecb86283c05d52f0a616a3de
Binary files /dev/null and b/test/data/s2_10m_labels_A.tif differ
diff --git a/test/data/s2_10m_labels_B.tif b/test/data/s2_10m_labels_B.tif
new file mode 100644
index 0000000000000000000000000000000000000000..de91615723f14adb16ac024fce92b1be32f4103b
Binary files /dev/null and b/test/data/s2_10m_labels_B.tif differ
diff --git a/test/data/s2_10m_patches_A.tif b/test/data/s2_10m_patches_A.tif
new file mode 100644
index 0000000000000000000000000000000000000000..c0567ff9282fb6628a1d9200fd9d63143b1c2487
Binary files /dev/null and b/test/data/s2_10m_patches_A.tif differ
diff --git a/test/data/s2_10m_patches_B.tif b/test/data/s2_10m_patches_B.tif
new file mode 100644
index 0000000000000000000000000000000000000000..056fe19ee93c6a892bb78f9174e014d0377ba3a9
Binary files /dev/null and b/test/data/s2_10m_patches_B.tif differ
diff --git a/test/data/s2_20m_patches_A.tif b/test/data/s2_20m_patches_A.tif
new file mode 100644
index 0000000000000000000000000000000000000000..2f299c2f5b1b4eed702d0c7d9bb542169b760434
Binary files /dev/null and b/test/data/s2_20m_patches_A.tif differ
diff --git a/test/data/s2_20m_patches_B.tif b/test/data/s2_20m_patches_B.tif
new file mode 100644
index 0000000000000000000000000000000000000000..afd4ac9775c191983af6cbea1da82943bace7be2
Binary files /dev/null and b/test/data/s2_20m_patches_B.tif differ
diff --git a/test/data/s2_20m_stack.jp2 b/test/data/s2_20m_stack.jp2
new file mode 100644
index 0000000000000000000000000000000000000000..c518a4ba71845802ebd6f443d18f626da22e5175
Binary files /dev/null and b/test/data/s2_20m_stack.jp2 differ
diff --git a/test/data/s2_labels_A.tif b/test/data/s2_labels_A.tif
new file mode 100644
index 0000000000000000000000000000000000000000..c4451320fad48a811d7b9a1b221502013d4a822f
Binary files /dev/null and b/test/data/s2_labels_A.tif differ
diff --git a/test/data/s2_labels_B.tif b/test/data/s2_labels_B.tif
new file mode 100644
index 0000000000000000000000000000000000000000..2b90eb45f97cf3e65045fcca00b95ec8aa7c0a77
Binary files /dev/null and b/test/data/s2_labels_B.tif differ
diff --git a/test/data/s2_patches_A.tif b/test/data/s2_patches_A.tif
new file mode 100644
index 0000000000000000000000000000000000000000..4f338e312214e89bf85e4aafe4b20588918dcc6f
Binary files /dev/null and b/test/data/s2_patches_A.tif differ
diff --git a/test/data/s2_patches_B.tif b/test/data/s2_patches_B.tif
new file mode 100644
index 0000000000000000000000000000000000000000..022d525e31db3713f4f10264411a0cfbbe76cf74
Binary files /dev/null and b/test/data/s2_patches_B.tif differ
diff --git a/test/data/s2_stack.jp2 b/test/data/s2_stack.jp2
new file mode 100644
index 0000000000000000000000000000000000000000..cd5864ee2583441036aeec6bce96eec6b0533ebd
Binary files /dev/null and b/test/data/s2_stack.jp2 differ
diff --git a/test/data/terrain_truth_epsg32654_A.tif b/test/data/terrain_truth_epsg32654_A.tif
new file mode 100644
index 0000000000000000000000000000000000000000..87a9a74bd6a337cac61559e2682b53676fecbd66
Binary files /dev/null and b/test/data/terrain_truth_epsg32654_A.tif differ
diff --git a/test/data/terrain_truth_epsg32654_B.tif b/test/data/terrain_truth_epsg32654_B.tif
new file mode 100644
index 0000000000000000000000000000000000000000..2114099b6a815fd3fd5d74449488e8e4ed98ca19
Binary files /dev/null and b/test/data/terrain_truth_epsg32654_B.tif differ
diff --git a/test/sr4rs_unittest.py b/test/sr4rs_unittest.py
index fbb921f8451cc83b3fd7b9e9e90bf61755511eca..89c3945f153304d04d35c23ef34513cf668120bc 100644
--- a/test/sr4rs_unittest.py
+++ b/test/sr4rs_unittest.py
@@ -4,8 +4,7 @@
import unittest
import os
from pathlib import Path
-import gdal
-import otbApplication as otb
+import test_utils
def command_train_succeed(extra_opts=""):
@@ -54,21 +53,7 @@ class SR4RSv1Test(unittest.TestCase):
command += "--output '{}?&box=256:256:512:512'".format(out_img)
os.system(command)
- nbchannels_reconstruct = gdal.Open(out_img).RasterCount
- nbchannels_baseline = gdal.Open(baseline).RasterCount
-
- self.assertTrue(nbchannels_reconstruct == nbchannels_baseline)
-
- for i in range(1, 1 + nbchannels_baseline):
- comp = otb.Registry.CreateApplication('CompareImages')
- comp.SetParameterString('ref.in', baseline)
- comp.SetParameterInt('ref.channel', i)
- comp.SetParameterString('meas.in', out_img)
- comp.SetParameterInt('meas.channel', i)
- comp.Execute()
- mae = comp.GetParameterFloat('mae')
-
- self.assertTrue(mae < 0.01)
+ self.assertTrue(test_utils.compare(baseline, out_img))
if __name__ == '__main__':
diff --git a/test/test_utils.py b/test/test_utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..c07301e91bb2eab4a808d53beaa46396c3ea82fc
--- /dev/null
+++ b/test/test_utils.py
@@ -0,0 +1,56 @@
+import otbApplication
+import os
+
+
+def get_nb_of_channels(raster):
+ """
+ Return the number of channels in the input raster
+ :param raster: raster filename (str)
+ :return the number of channels in the image (int)
+ """
+ info = otbApplication.Registry.CreateApplication("ReadImageInfo")
+ info.SetParameterString("in", raster)
+ info.ExecuteAndWriteOutput()
+ return info.GetParameterInt('numberbands')
+
+
+def compare(raster1, raster2, tol=0.01):
+ """
+ Return True if the two rasters have the same contents in each bands
+ :param raster1: raster 1 filename (str)
+ :param raster2: raster 2 filename (str)
+ :param tol: tolerance (float)
+ """
+ n_bands1 = get_nb_of_channels(raster1)
+ n_bands2 = get_nb_of_channels(raster2)
+ if n_bands1 != n_bands2:
+ print("The images have not the same number of channels")
+ return False
+
+ for i in range(1, 1 + n_bands1):
+ comp = otbApplication.Registry.CreateApplication('CompareImages')
+ comp.SetParameterString('ref.in', raster1)
+ comp.SetParameterInt('ref.channel', i)
+ comp.SetParameterString('meas.in', raster2)
+ comp.SetParameterInt('meas.channel', i)
+ comp.Execute()
+ mae = comp.GetParameterFloat('mae')
+ if mae > tol:
+ print("The images have not the same content in channel {} "
+ "(Mean average error: {})".format(i, mae))
+ return False
+ return True
+
+
+def resolve_paths(filename, var_list):
+ """
+ Retrieve environment variables in paths
+ :param filename: file name
+ :params var_list: variable list
+ :return filename with retrieved environment variables
+ """
+ new_filename = filename
+ for var in var_list:
+ new_filename = new_filename.replace("${}".format(var), os.environ[var])
+ print("Resolve filename...\n\tfilename: {}, \n\tnew filename: {}".format(filename, new_filename))
+ return new_filename
diff --git a/test/tutorial_unittest.py b/test/tutorial_unittest.py
new file mode 100644
index 0000000000000000000000000000000000000000..7934862f348326de13a11eef4c81a4fe6512cec6
--- /dev/null
+++ b/test/tutorial_unittest.py
@@ -0,0 +1,513 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+import pytest
+import unittest
+import os
+from pathlib import Path
+import test_utils
+
+INFERENCE_MAE_TOL = 10.0 # Dummy value: we don't really care of the mae value but rather the image size etc
+
+
+def resolve_paths(path):
+ """
+ Resolve a path with the environment variables
+ """
+ return test_utils.resolve_paths(path, var_list=["TMPDIR", "DATADIR"])
+
+
+def run_command(command):
+ """
+ Run a command
+ :param command: the command to run
+ """
+ full_command = resolve_paths(command)
+ print("Running command: \n\t {}".format(full_command))
+ os.system(full_command)
+
+
+def run_command_and_test_exist(command, file_list):
+ """
+ :param command: the command to run (str)
+ :param file_list: list of files to check
+ :return True or False
+ """
+ run_command(command)
+ print("Checking if files exist...")
+ for file in file_list:
+ print("\t{}".format(file))
+ path = Path(resolve_paths(file))
+ if not path.is_file():
+ print("File {} does not exist!".format(file))
+ return False
+ print("\tOk")
+ return True
+
+
+def run_command_and_compare(command, to_compare_dict, tol=0.01):
+ """
+ :param command: the command to run (str)
+ :param to_compare_dict: a dict of {baseline1: output1, ..., baselineN: outputN}
+ :param tol: tolerance (float)
+ :return True or False
+ """
+
+ run_command(command)
+ for baseline, output in to_compare_dict.items():
+ if not test_utils.compare(resolve_paths(baseline), resolve_paths(output), tol):
+ print("Baseline {} and output {} differ.".format(baseline, output))
+ return False
+ return True
+
+
+class TutorialTest(unittest.TestCase):
+
+ @pytest.mark.order(1)
+ def test_sample_selection(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_LabelImageSampleSelection "
+ "-inref $DATADIR/terrain_truth_epsg32654_A.tif "
+ "-nodata 255 "
+ "-outvec $TMPDIR/outvec_A.gpkg",
+ file_list=["$TMPDIR/outvec_A.gpkg"]))
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_LabelImageSampleSelection "
+ "-inref $DATADIR/terrain_truth_epsg32654_B.tif "
+ "-nodata 255 "
+ "-outvec $TMPDIR/outvec_B.gpkg",
+ file_list=["$TMPDIR/outvec_B.gpkg"]))
+
+ @pytest.mark.order(2)
+ def test_patches_extraction(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command="otbcli_PatchesExtraction "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.out $TMPDIR/s2_patches_A.tif "
+ "-source1.patchsizex 16 "
+ "-source1.patchsizey 16 "
+ "-vec $TMPDIR/outvec_A.gpkg "
+ "-field class "
+ "-outlabels $TMPDIR/s2_labels_A.tif",
+ to_compare_dict={"$DATADIR/s2_patches_A.tif": "$TMPDIR/s2_patches_A.tif",
+ "$DATADIR/s2_labels_A.tif": "$TMPDIR/s2_labels_A.tif"}))
+ self.assertTrue(
+ run_command_and_compare(
+ command="otbcli_PatchesExtraction "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.out $TMPDIR/s2_patches_B.tif "
+ "-source1.patchsizex 16 "
+ "-source1.patchsizey 16 "
+ "-vec $TMPDIR/outvec_B.gpkg "
+ "-field class "
+ "-outlabels $TMPDIR/s2_labels_B.tif",
+ to_compare_dict={"$DATADIR/s2_patches_B.tif": "$TMPDIR/s2_patches_B.tif",
+ "$DATADIR/s2_labels_B.tif": "$TMPDIR/s2_labels_B.tif"}))
+
+ @pytest.mark.order(3)
+ def test_generate_model1(self):
+ run_command("git clone https://github.com/remicres/otbtf_tutorials_resources.git "
+ "$TMPDIR/otbtf_tuto_repo")
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="python $TMPDIR/otbtf_tuto_repo/01_patch_based_classification/models/create_model1.py "
+ "$TMPDIR/model1",
+ file_list=["$TMPDIR/model1/saved_model.pb"]))
+
+ @pytest.mark.order(4)
+ def test_model1_train(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_TensorflowModelTrain "
+ "-training.source1.il $DATADIR/s2_patches_A.tif "
+ "-training.source1.patchsizex 16 "
+ "-training.source1.patchsizey 16 "
+ "-training.source1.placeholder x "
+ "-training.source2.il $DATADIR/s2_labels_A.tif "
+ "-training.source2.patchsizex 1 "
+ "-training.source2.patchsizey 1 "
+ "-training.source2.placeholder y "
+ "-model.dir $TMPDIR/model1 "
+ "-training.targetnodes optimizer "
+ "-training.epochs 10 "
+ "-validation.mode class "
+ "-validation.source1.il $DATADIR/s2_patches_B.tif "
+ "-validation.source1.name x "
+ "-validation.source2.il $DATADIR/s2_labels_B.tif "
+ "-validation.source2.name prediction "
+ "-model.saveto $TMPDIR/model1/variables/variables",
+ file_list=["$TMPDIR/model1/variables/variables.index"]
+ )
+ )
+
+ @pytest.mark.order(5)
+ def test_model1_inference_pb(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command="otbcli_TensorflowModelServe "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.rfieldx 16 "
+ "-source1.rfieldy 16 "
+ "-source1.placeholder x "
+ "-model.dir $TMPDIR/model1 "
+ "-output.names prediction "
+ "-out \"$TMPDIR/classif_model1.tif?&box=4000:4000:1000:1000\" uint8",
+ to_compare_dict={"$DATADIR/classif_model1.tif": "$TMPDIR/classif_model1.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+ @pytest.mark.order(6)
+ def test_model1_inference_fcn(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command="otbcli_TensorflowModelServe "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.rfieldx 16 "
+ "-source1.rfieldy 16 "
+ "-source1.placeholder x "
+ "-model.dir $TMPDIR/model1 "
+ "-output.names prediction "
+ "-model.fullyconv on "
+ "-output.spcscale 4 "
+ "-out \"$TMPDIR/classif_model1.tif?&box=1000:1000:256:256\" uint8",
+ to_compare_dict={"$DATADIR/classif_model1.tif": "$TMPDIR/classif_model1.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+ @pytest.mark.order(7)
+ def test_rf_sampling(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_SampleExtraction "
+ "-in $DATADIR/s2_stack.jp2 "
+ "-vec $TMPDIR/outvec_A.gpkg "
+ "-field class "
+ "-out $TMPDIR/pixelvalues_A.gpkg",
+ file_list=["$TMPDIR/pixelvalues_A.gpkg"]))
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_SampleExtraction "
+ "-in $DATADIR/s2_stack.jp2 "
+ "-vec $TMPDIR/outvec_B.gpkg "
+ "-field class "
+ "-out $TMPDIR/pixelvalues_B.gpkg",
+ file_list=["$TMPDIR/pixelvalues_B.gpkg"]))
+
+ @pytest.mark.order(8)
+ def test_rf_training(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_TrainVectorClassifier "
+ "-io.vd $TMPDIR/pixelvalues_A.gpkg "
+ "-valid.vd $TMPDIR/pixelvalues_B.gpkg "
+ "-feat value_0 value_1 value_2 value_3 "
+ "-cfield class "
+ "-classifier rf "
+ "-io.out $TMPDIR/randomforest_model.yaml ",
+ file_list=["$TMPDIR/randomforest_model.yaml"]))
+
+ @pytest.mark.order(9)
+ def test_generate_model2(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="python $TMPDIR/otbtf_tuto_repo/01_patch_based_classification/models/create_model2.py "
+ "$TMPDIR/model2",
+ file_list=["$TMPDIR/model2/saved_model.pb"]))
+
+ @pytest.mark.order(10)
+ def test_model2_train(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_TensorflowModelTrain "
+ "-training.source1.il $DATADIR/s2_patches_A.tif "
+ "-training.source1.patchsizex 16 "
+ "-training.source1.patchsizey 16 "
+ "-training.source1.placeholder x "
+ "-training.source2.il $DATADIR/s2_labels_A.tif "
+ "-training.source2.patchsizex 1 "
+ "-training.source2.patchsizey 1 "
+ "-training.source2.placeholder y "
+ "-model.dir $TMPDIR/model2 "
+ "-training.targetnodes optimizer "
+ "-training.epochs 10 "
+ "-validation.mode class "
+ "-validation.source1.il $DATADIR/s2_patches_B.tif "
+ "-validation.source1.name x "
+ "-validation.source2.il $DATADIR/s2_labels_B.tif "
+ "-validation.source2.name prediction "
+ "-model.saveto $TMPDIR/model2/variables/variables",
+ file_list=["$TMPDIR/model2/variables/variables.index"]))
+
+ @pytest.mark.order(11)
+ def test_model2_inference_fcn(self):
+ self.assertTrue(
+ run_command_and_compare(command="otbcli_TensorflowModelServe "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.rfieldx 16 "
+ "-source1.rfieldy 16 "
+ "-source1.placeholder x "
+ "-model.dir $TMPDIR/model2 "
+ "-model.fullyconv on "
+ "-output.names prediction "
+ "-out \"$TMPDIR/classif_model2.tif?&box=4000:4000:1000:1000\" uint8",
+ to_compare_dict={"$DATADIR/classif_model2.tif": "$TMPDIR/classif_model2.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+ @pytest.mark.order(12)
+ def test_model2rf_train(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_TrainClassifierFromDeepFeatures "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.rfieldx 16 "
+ "-source1.rfieldy 16 "
+ "-source1.placeholder x "
+ "-model.dir $TMPDIR/model2 "
+ "-model.fullyconv on "
+ "-optim.tilesizex 999999 "
+ "-optim.tilesizey 128 "
+ "-output.names features "
+ "-vd $TMPDIR/outvec_A.gpkg "
+ "-valid $TMPDIR/outvec_B.gpkg "
+ "-sample.vfn class "
+ "-sample.bm 0 "
+ "-classifier rf "
+ "-out $TMPDIR/RF_model_from_deep_features.yaml",
+ file_list=["$TMPDIR/RF_model_from_deep_features.yaml"]))
+
+ @pytest.mark.order(13)
+ def test_model2rf_inference(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command="otbcli_ImageClassifierFromDeepFeatures "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.rfieldx 16 "
+ "-source1.rfieldy 16 "
+ "-source1.placeholder x "
+ "-deepmodel.dir $TMPDIR/model2 "
+ "-deepmodel.fullyconv on "
+ "-output.names features "
+ "-model $TMPDIR/RF_model_from_deep_features.yaml "
+ "-out \"$TMPDIR/RF_model_from_deep_features_map.tif?&box=4000:4000:1000:1000\" uint8",
+ to_compare_dict={
+ "$DATADIR/RF_model_from_deep_features_map.tif": "$TMPDIR/RF_model_from_deep_features_map.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+ @pytest.mark.order(14)
+ def test_patch_extraction_20m(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command="OTB_TF_NSOURCES=2 otbcli_PatchesExtraction "
+ "-source1.il $DATADIR/s2_20m_stack.jp2 "
+ "-source1.patchsizex 8 "
+ "-source1.patchsizey 8 "
+ "-source1.out $TMPDIR/s2_20m_patches_A.tif "
+ "-source2.il $DATADIR/s2_stack.jp2 "
+ "-source2.patchsizex 16 "
+ "-source2.patchsizey 16 "
+ "-source2.out $TMPDIR/s2_10m_patches_A.tif "
+ "-vec $TMPDIR/outvec_A.gpkg "
+ "-field class "
+ "-outlabels $TMPDIR/s2_10m_labels_A.tif uint8",
+ to_compare_dict={"$DATADIR/s2_10m_labels_A.tif": "$TMPDIR/s2_10m_labels_A.tif",
+ "$DATADIR/s2_10m_patches_A.tif": "$TMPDIR/s2_10m_patches_A.tif",
+ "$DATADIR/s2_20m_patches_A.tif": "$TMPDIR/s2_20m_patches_A.tif"}))
+ self.assertTrue(
+ run_command_and_compare(
+ command="OTB_TF_NSOURCES=2 otbcli_PatchesExtraction "
+ "-source1.il $DATADIR/s2_20m_stack.jp2 "
+ "-source1.patchsizex 8 "
+ "-source1.patchsizey 8 "
+ "-source1.out $TMPDIR/s2_20m_patches_B.tif "
+ "-source2.il $DATADIR/s2_stack.jp2 "
+ "-source2.patchsizex 16 "
+ "-source2.patchsizey 16 "
+ "-source2.out $TMPDIR/s2_10m_patches_B.tif "
+ "-vec $TMPDIR/outvec_B.gpkg "
+ "-field class "
+ "-outlabels $TMPDIR/s2_10m_labels_B.tif uint8",
+ to_compare_dict={"$DATADIR/s2_10m_labels_B.tif": "$TMPDIR/s2_10m_labels_B.tif",
+ "$DATADIR/s2_10m_patches_B.tif": "$TMPDIR/s2_10m_patches_B.tif",
+ "$DATADIR/s2_20m_patches_B.tif": "$TMPDIR/s2_20m_patches_B.tif"}))
+
+ @pytest.mark.order(15)
+ def test_generate_model3(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="python $TMPDIR/otbtf_tuto_repo/01_patch_based_classification/models/create_model3.py "
+ "$TMPDIR/model3",
+ file_list=["$TMPDIR/model3/saved_model.pb"]))
+
+ @pytest.mark.order(16)
+ def test_model3_train(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="OTB_TF_NSOURCES=2 otbcli_TensorflowModelTrain "
+ "-training.source1.il $DATADIR/s2_20m_patches_A.tif "
+ "-training.source1.patchsizex 8 "
+ "-training.source1.patchsizey 8 "
+ "-training.source1.placeholder x1 "
+ "-training.source2.il $DATADIR/s2_10m_patches_A.tif "
+ "-training.source2.patchsizex 16 "
+ "-training.source2.patchsizey 16 "
+ "-training.source2.placeholder x2 "
+ "-training.source3.il $DATADIR/s2_10m_labels_A.tif "
+ "-training.source3.patchsizex 1 "
+ "-training.source3.patchsizey 1 "
+ "-training.source3.placeholder y "
+ "-model.dir $TMPDIR/model3 "
+ "-training.targetnodes optimizer "
+ "-training.epochs 10 "
+ "-validation.mode class "
+ "-validation.source1.il $DATADIR/s2_20m_patches_B.tif "
+ "-validation.source1.name x1 "
+ "-validation.source2.il $DATADIR/s2_10m_patches_B.tif "
+ "-validation.source2.name x2 "
+ "-validation.source3.il $DATADIR/s2_10m_labels_B.tif "
+ "-validation.source3.name prediction "
+ "-model.saveto $TMPDIR/model3/variables/variables",
+ file_list=["$TMPDIR/model3/variables/variables.index"]))
+
+ @pytest.mark.order(17)
+ def test_model3_inference_pb(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command=
+ "OTB_TF_NSOURCES=2 otbcli_TensorflowModelServe "
+ "-source1.il $DATADIR/s2_20m_stack.jp2 "
+ "-source1.rfieldx 8 "
+ "-source1.rfieldy 8 "
+ "-source1.placeholder x1 "
+ "-source2.il $DATADIR/s2_stack.jp2 "
+ "-source2.rfieldx 16 "
+ "-source2.rfieldy 16 "
+ "-source2.placeholder x2 "
+ "-model.dir $TMPDIR/model3 "
+ "-output.names prediction "
+ "-out \"$TMPDIR/classif_model3_pb.tif?&box=2000:2000:500:500&gdal:co:compress=deflate\"",
+ to_compare_dict={"$DATADIR/classif_model3_pb.tif": "$TMPDIR/classif_model3_pb.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+ @pytest.mark.order(18)
+ def test_model3_inference_fcn(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command=
+ "OTB_TF_NSOURCES=2 otbcli_TensorflowModelServe "
+ "-source1.il $DATADIR/s2_20m_stack.jp2 "
+ "-source1.rfieldx 8 "
+ "-source1.rfieldy 8 "
+ "-source1.placeholder x1 "
+ "-source2.il $DATADIR/s2_stack.jp2 "
+ "-source2.rfieldx 16 "
+ "-source2.rfieldy 16 "
+ "-source2.placeholder x2 "
+ "-model.dir $TMPDIR/model3 "
+ "-model.fullyconv on "
+ "-output.names prediction "
+ "-out \"$TMPDIR/classif_model3_fcn.tif?&box=2000:2000:500:500&gdal:co:compress=deflate\"",
+ to_compare_dict={"$DATADIR/classif_model3_fcn.tif": "$TMPDIR/classif_model3_fcn.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+ @pytest.mark.order(19)
+ def test_generate_model4(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="python $TMPDIR/otbtf_tuto_repo/02_semantic_segmentation/models/create_model4.py "
+ "$TMPDIR/model4",
+ file_list=["$TMPDIR/model4/saved_model.pb"]))
+
+ @pytest.mark.order(20)
+ def test_patches_selection_semseg(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_PatchesSelection "
+ "-in $DATADIR/fake_spot6.jp2 "
+ "-grid.step 64 "
+ "-grid.psize 64 "
+ "-outtrain $TMPDIR/outvec_A_semseg.gpkg "
+ "-outvalid $TMPDIR/outvec_B_semseg.gpkg",
+ file_list=["$TMPDIR/outvec_A_semseg.gpkg",
+ "$TMPDIR/outvec_B_semseg.gpkg"]))
+
+ @pytest.mark.order(21)
+ def test_patch_extraction_semseg(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command="OTB_TF_NSOURCES=2 otbcli_PatchesExtraction "
+ "-source1.il $DATADIR/fake_spot6.jp2 "
+ "-source1.patchsizex 64 "
+ "-source1.patchsizey 64 "
+ "-source1.out \"$TMPDIR/amsterdam_patches_A.tif?&gdal:co:compress=deflate\" "
+ "-source2.il $TMPDIR/otbtf_tuto_repo/02_semantic_segmentation/"
+ "amsterdam_dataset/terrain_truth/amsterdam_labelimage.tif "
+ "-source2.patchsizex 64 "
+ "-source2.patchsizey 64 "
+ "-source2.out \"$TMPDIR/amsterdam_labels_A.tif?&gdal:co:compress=deflate\" "
+ "-vec $TMPDIR/outvec_A_semseg.gpkg "
+ "-field id ",
+ to_compare_dict={"$DATADIR/amsterdam_labels_A.tif": "$TMPDIR/amsterdam_labels_A.tif",
+ "$DATADIR/amsterdam_patches_A.tif": "$TMPDIR/amsterdam_patches_A.tif"}))
+ self.assertTrue(
+ run_command_and_compare(
+ command="OTB_TF_NSOURCES=2 otbcli_PatchesExtraction "
+ "-source1.il $DATADIR/fake_spot6.jp2 "
+ "-source1.patchsizex 64 "
+ "-source1.patchsizey 64 "
+ "-source1.out \"$TMPDIR/amsterdam_patches_B.tif?&gdal:co:compress=deflate\" "
+ "-source2.il $TMPDIR/otbtf_tuto_repo/02_semantic_segmentation/"
+ "amsterdam_dataset/terrain_truth/amsterdam_labelimage.tif "
+ "-source2.patchsizex 64 "
+ "-source2.patchsizey 64 "
+ "-source2.out \"$TMPDIR/amsterdam_labels_B.tif?&gdal:co:compress=deflate\" "
+ "-vec $TMPDIR/outvec_B_semseg.gpkg "
+ "-field id ",
+ to_compare_dict={"$DATADIR/amsterdam_labels_B.tif": "$TMPDIR/amsterdam_labels_B.tif",
+ "$DATADIR/amsterdam_patches_B.tif": "$TMPDIR/amsterdam_patches_B.tif"}))
+
+ @pytest.mark.order(22)
+ def test_model4_train(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="OTB_TF_NSOURCES=1 otbcli_TensorflowModelTrain "
+ "-training.source1.il $DATADIR/amsterdam_patches_A.tif "
+ "-training.source1.patchsizex 64 "
+ "-training.source1.patchsizey 64 "
+ "-training.source1.placeholder x "
+ "-training.source2.il $DATADIR/amsterdam_labels_A.tif "
+ "-training.source2.patchsizex 64 "
+ "-training.source2.patchsizey 64 "
+ "-training.source2.placeholder y "
+ "-model.dir $TMPDIR/model4 "
+ "-training.targetnodes optimizer "
+ "-training.epochs 10 "
+ "-validation.mode class "
+ "-validation.source1.il $DATADIR/amsterdam_patches_B.tif "
+ "-validation.source1.name x "
+ "-validation.source2.il $DATADIR/amsterdam_labels_B.tif "
+ "-validation.source2.name prediction "
+ "-model.saveto $TMPDIR/model4/variables/variables",
+ file_list=["$TMPDIR/model4/variables/variables.index"]))
+
+ @pytest.mark.order(23)
+ def test_model4_inference(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command=
+ "otbcli_TensorflowModelServe "
+ "-source1.il $DATADIR/fake_spot6.jp2 "
+ "-source1.rfieldx 64 "
+ "-source1.rfieldy 64 "
+ "-source1.placeholder x "
+ "-model.dir $TMPDIR/model4 "
+ "-model.fullyconv on "
+ "-output.names prediction_fcn "
+ "-output.efieldx 32 "
+ "-output.efieldy 32 "
+ "-out \"$TMPDIR/classif_model4.tif?&gdal:co:compress=deflate\" uint8",
+ to_compare_dict={"$DATADIR/classif_model4.tif": "$TMPDIR/classif_model4.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+
+if __name__ == '__main__':
+ unittest.main()