From adbf1a90d55aeff1acd1b481334e1c74f886f4d3 Mon Sep 17 00:00:00 2001
From: DaliCHEBBI <mohamed-ali.chebbi@ign.fr>
Date: Wed, 24 Sep 2025 18:26:03 +0200
Subject: [PATCH 1/6] add feature of difference between two folders

---
 altianalysis/compute_difference.py           | 22 ++++++---
 altianalysis/run_difference_with_gpao.py     | 48 +++++++++++++++-----
 altianalysis/run_difference_with_parallel.py | 31 ++++++++-----
 test/test_compute_difference.py              | 14 +++++-
 test/test_run_difference_with_gpao.py        |  4 +-
 test/test_run_difference_with_parallel.py    | 17 ++++++-
 6 files changed, 102 insertions(+), 34 deletions(-)

diff --git a/altianalysis/compute_difference.py b/altianalysis/compute_difference.py
index d4c76ad..60e41ac 100644
--- a/altianalysis/compute_difference.py
+++ b/altianalysis/compute_difference.py
@@ -13,6 +13,9 @@
 def parse_args():
     parser = argparse.ArgumentParser("compute difference map between lidar dtm and rge alti")
     parser.add_argument("--dtm_lidar_file", type=str, help="dtm lidar tif file")
+    parser.add_argument(
+        "--second_elevation_file", default=None, type=str, help="secondary elevation file when no stream to be used !"
+    )
     parser.add_argument("--name_save_out", type=str, help="name of difference file")
     return parser.parse_args()
 
@@ -91,16 +94,23 @@ def compute_difference_between_dtms(dtm_lidar_file: str, dtm_rge_tile: str, name
             dst.write(_difference, 1)
 
 
-def main(reference_dtm_file: Path | str, output_difference_file: Path | str):
+def main(reference_dtm_file: Path | str, secondary_dtm_file: Path | str | None, output_difference_file: Path | str):
 
-    with tempfile.NamedTemporaryFile(suffix="_dtm_rgealti.tif", delete=False) as tmp_rge:
+    if secondary_dtm_file:
+        compute_difference_between_dtms(reference_dtm_file, secondary_dtm_file, output_difference_file)
 
-        success = _extract_rge_alti_tile_from_stream(reference_dtm_file, pixel_per_meter=5, output_path=tmp_rge.name)
+    else:
 
-        if success:
-            compute_difference_between_dtms(reference_dtm_file, tmp_rge, output_difference_file)
+        with tempfile.NamedTemporaryFile(suffix="_dtm_rgealti.tif", delete=False) as tmp_rge:
+
+            success = _extract_rge_alti_tile_from_stream(
+                reference_dtm_file, pixel_per_meter=5, output_path=tmp_rge.name
+            )
+
+            if success:
+                compute_difference_between_dtms(reference_dtm_file, tmp_rge, output_difference_file)
 
 
 if __name__ == "__main__":
     args = parse_args()
-    main(args.dtm_lidar_file, args.name_save_out)
+    main(args.dtm_lidar_file, args.second_elevation_file, args.name_save_out)
diff --git a/altianalysis/run_difference_with_gpao.py b/altianalysis/run_difference_with_gpao.py
index 60311dd..9f2d405 100644
--- a/altianalysis/run_difference_with_gpao.py
+++ b/altianalysis/run_difference_with_gpao.py
@@ -25,23 +25,37 @@ def get_tile_names(folder: Path) -> List[str]:
     return filenames
 
 
-def create_one_job_one_difference(store: Store, dir_in: Path, input_file: str, output: Path):
+def create_one_job_one_difference(store: Store, dir_in: Path, second_dir: Path | None, input_file: str, output: Path):
     job_name = f"difference_{input_file}"
-    command = f"""
-docker run -t --rm --userns=host --shm-size=2gb
--v {store.to_unix(dir_in)}:/input
--v {store.to_unix(output)}:/output
-ghcr.io/ignf/altianalysis:{__version__}
-python -m altianalysis.compute_difference
---dtm_lidar_file /input/{input_file}
---name_save_out /output/{input_file}
-"""
+    if second_dir is not None:
+        command = f"""
+    docker run -t --rm --userns=host --shm-size=2gb
+    -v {store.to_unix(dir_in)}:/input
+    -v {store.to_unix(second_dir)}:/second_input
+    -v {store.to_unix(output)}:/output
+    ghcr.io/ignf/altianalysis:{__version__}
+    python -m altianalysis.compute_difference
+    --dtm_lidar_file /input/{input_file}
+    --second_elevation_file /second_input{input_file}
+    --name_save_out /output/{input_file}
+    """
+    else:
+        command = f"""
+    docker run -t --rm --userns=host --shm-size=2gb
+    -v {store.to_unix(dir_in)}:/input
+    -v {store.to_unix(output)}:/output
+    ghcr.io/ignf/altianalysis:{__version__}
+    python -m altianalysis.compute_difference
+    --dtm_lidar_file /input/{input_file}
+    --name_save_out /output/{input_file}
+    """
     job = Job(job_name, command, tags=["docker"])
     return job
 
 
 def create_gpao_project(
     dtms_lhd: Path,
+    secondary_dir: Path | None,
     out: Path,
     store: Store,
     project_name: str,
@@ -63,7 +77,7 @@ def create_gpao_project(
     jobs = []
 
     for tile_ in dtm_tile_names:
-        job = create_one_job_one_difference(store, dtms_lhd, tile_, out)
+        job = create_one_job_one_difference(store, dtms_lhd, secondary_dir, tile_, out)
         jobs.append(job)
 
     # create the project
@@ -72,6 +86,7 @@ def create_gpao_project(
 
 def compute_on_gpao(
     dtms_lhd: Path,
+    secondary_dir: Path | None,
     out: Path,
     gpao_hostname: str,
     local_store_path: Path,
@@ -85,7 +100,7 @@ def compute_on_gpao(
 
     logging.debug(f"Local store path ({local_store_path}) converted to client store path ({runner_store_path})")
 
-    project = create_gpao_project(dtms_lhd, out, store, project_name)
+    project = create_gpao_project(dtms_lhd, secondary_dir, out, store, project_name)
     builder = Builder([project])
 
     builder.save_as_json(out / "gpao_project.json")
@@ -104,6 +119,14 @@ def parse_args():
         required=True,
         help="Dossier des dalles MNT Lidar HD",
     )
+    parser.add_argument(
+        "-i",
+        "--secondary_dtm_dir",
+        type=Path,
+        default=None,
+        help="Dossier du second des MNT pour calculer la différence",
+    )
+
     parser.add_argument(
         "-o",
         "--out",
@@ -139,6 +162,7 @@ def parse_args():
 
     compute_on_gpao(
         args.dtm_lhd_dir,
+        args.secondary_dtm_dir,
         args.out,
         args.gpao_hostname,
         args.local_store_path,
diff --git a/altianalysis/run_difference_with_parallel.py b/altianalysis/run_difference_with_parallel.py
index db76947..8ba2df1 100644
--- a/altianalysis/run_difference_with_parallel.py
+++ b/altianalysis/run_difference_with_parallel.py
@@ -1,38 +1,36 @@
 import argparse
 import os
-import tempfile
 from pathlib import Path
 
 from joblib import Parallel, delayed
 
-from altianalysis.compute_difference import _extract_rge_alti_tile_from_stream, compute_difference_between_dtms
+from altianalysis.compute_difference import main
 
 
-def _compute_one_difference(dtm_lhd_file: str, _dir: Path, _out_dir_difference: Path):
+def _compute_one_difference(dtm_lhd_file: str, _dir: Path, _out_dir_difference: Path, second_dir=None):
 
     full_dtm_file = os.path.join(_dir, dtm_lhd_file)
     full_difference_file = os.path.join(_out_dir_difference, dtm_lhd_file)
+    _second_file = None
 
-    # compute difference for individual files
-    with tempfile.NamedTemporaryFile(suffix="_dtm_rgealti.tif", delete=False) as tmp_rge:
+    if second_dir is not None:
+        _second_file = os.path.join(second_dir, dtm_lhd_file)
 
-        success = _extract_rge_alti_tile_from_stream(full_dtm_file, tmp_rge.name)
-        if success:
-            compute_difference_between_dtms(full_dtm_file, tmp_rge.name, full_difference_file)
+    main(full_dtm_file, _second_file, full_difference_file)
 
 
-def compute_all_difference_maps(_dir: Path, _out_dir_difference: Path):
+def compute_all_difference_maps(_dir: Path, _second_dir: Path | None, _out_dir_difference: Path):
 
     os.makedirs(_out_dir_difference, exist_ok=True)
     all_dtm_lhd_names = []
-
     for dtm_file in _dir.iterdir():
         if dtm_file.is_file() and (str(dtm_file).endswith(".tif") or str(dtm_file).endswith(".TIF")):
             all_dtm_lhd_names.append(dtm_file.name)
 
     # bulk compute
     _ = Parallel(n_jobs=12, verbose=True)(
-        delayed(_compute_one_difference)(dtm_lhd_file, _dir, _out_dir_difference) for dtm_lhd_file in all_dtm_lhd_names
+        delayed(_compute_one_difference)(dtm_lhd_file, _dir, _out_dir_difference, second_dir=_second_dir)
+        for dtm_lhd_file in all_dtm_lhd_names
     )
 
 
@@ -45,6 +43,15 @@ def parse_args():
         required=True,
         help="Dossier des dalles MNT Lidar HD",
     )
+
+    parser.add_argument(
+        "-s",
+        "--secondary_dtm_elevation_dir",
+        type=Path,
+        default=None,
+        help="Dossier contenant le second ensemble de dalles MNT pour le calcul de différence",
+    )
+
     parser.add_argument(
         "-o",
         "--name_dir_difference",
@@ -58,4 +65,4 @@ def parse_args():
 
 if __name__ == "__main__":
     args = parse_args()
-    compute_all_difference_maps(args.dtm_lidar_dir, args.name_dir_difference)
+    compute_all_difference_maps(args.dtm_lidar_dir, args.secondary_dtm_elevation_dir, args.name_dir_difference)
diff --git a/test/test_compute_difference.py b/test/test_compute_difference.py
index ffe303e..f4c041f 100644
--- a/test/test_compute_difference.py
+++ b/test/test_compute_difference.py
@@ -166,8 +166,20 @@ def test_main():
     output_dir.mkdir()
     dtm_lidar_file = "./data/lhd/Semis_2021_0886_6443_LA93_IGN69_50CM.tif"
 
+    second_dtm_file = "./data/lhd/Semis_2021_0886_6443_LA93_IGN69_50CM.tif"
+
     out_difference_file = output_dir / "Difference_with_rge_Semis_2021_0886_6443_LA93_IGN69_50CM.tif"
+    out_difference_file_with_self = output_dir / "Difference_self_with_rge_Semis_2021_0886_6443_LA93_IGN69_50CM.tif"
 
-    compute_difference.main(dtm_lidar_file, out_difference_file)
+    compute_difference.main(dtm_lidar_file, None, out_difference_file)
 
     assert os.path.exists(out_difference_file), "difference with rge alti not computed !"
+
+    # run with secondary file
+    compute_difference.main(dtm_lidar_file, second_dtm_file, out_difference_file_with_self)
+
+    assert os.path.exists(out_difference_file_with_self), "difference with self is not computed"
+
+    with rasterio.open(out_difference_file_with_self) as o_diff_self:
+        diff = o_diff_self.read()
+        assert np.all(diff == 0), "difference with self yields null values"
diff --git a/test/test_run_difference_with_gpao.py b/test/test_run_difference_with_gpao.py
index b0aa244..75804a2 100644
--- a/test/test_run_difference_with_gpao.py
+++ b/test/test_run_difference_with_gpao.py
@@ -28,7 +28,7 @@ def test_create_gpao_project():
     output_dir = TMP_PATH / "create_gpao_project"
     dtm_lidar_lhds = Path("./data/lhd_dir_gpao")
     project_name = "test_create_gpao_project_difference_with_dem_rge_alti"
-    project = run_difference_with_gpao.create_gpao_project(dtm_lidar_lhds, output_dir, STORE, project_name)
+    project = run_difference_with_gpao.create_gpao_project(dtm_lidar_lhds, None, output_dir, STORE, project_name)
 
     assert project is not None
 
@@ -53,7 +53,7 @@ def test_gpao_run():
     local_store_path = Path("data/lhd_dir_gpao").resolve()
 
     run_difference_with_gpao.compute_on_gpao(
-        Path(dtm_lidar_lhds), Path(output_dir), gpao_hostname, local_store_path, runner_store_path, project_name
+        Path(dtm_lidar_lhds), None, Path(output_dir), gpao_hostname, local_store_path, runner_store_path, project_name
     )
 
     if gpao_hostname == "localhost":
diff --git a/test/test_run_difference_with_parallel.py b/test/test_run_difference_with_parallel.py
index ff0332a..f1746ad 100644
--- a/test/test_run_difference_with_parallel.py
+++ b/test/test_run_difference_with_parallel.py
@@ -19,7 +19,8 @@ def test_compute_all_difference_maps():
     output_dir = TMP_PATH / "compute_all_difference_maps"
     output_dir.mkdir()
     dtm_lidar_dir = Path("./data/lhd_dir_gpao")
-    run_difference_with_parallel.compute_all_difference_maps(dtm_lidar_dir, output_dir)
+
+    run_difference_with_parallel.compute_all_difference_maps(dtm_lidar_dir, None, output_dir)
 
     # check all difference maps are computed and stored in output_dir
     for lidar_dtm_file in dtm_lidar_dir.iterdir():
@@ -29,3 +30,17 @@ def test_compute_all_difference_maps():
             assert os.path.exists(_matching_difference_file), "Difference file of {} is not computed!".format(
                 lidar_dtm_file
             )
+
+    # second test with secondary folder of dtm files holding the same names
+    output_dir_with_sec = TMP_PATH / "compute_all_difference_maps"
+    sec_dtm_dir = Path("./data/lhd_dir_gpao")
+
+    run_difference_with_parallel.compute_all_difference_maps(dtm_lidar_dir, sec_dtm_dir, output_dir_with_sec)
+
+    for lidar_dtm_file in dtm_lidar_dir.iterdir():
+        if lidar_dtm_file.is_file() and str(lidar_dtm_file).endswith(".tif"):
+            # check if corresponding difference file exists
+            _matching_difference_file = output_dir_with_sec / lidar_dtm_file.name
+            assert os.path.exists(_matching_difference_file), "Difference file of {} is not computed!".format(
+                lidar_dtm_file
+            )

From 6cc4b82e648f7507efe93b9d465dc228a147ea9d Mon Sep 17 00:00:00 2001
From: DaliCHEBBI <mohamed-ali.chebbi@ign.fr>
Date: Thu, 25 Sep 2025 09:22:49 +0200
Subject: [PATCH 2/6] rename test outputs

---
 test/test_run_difference_with_gpao.py | 33 +++++++++++++++++++++++++--
 1 file changed, 31 insertions(+), 2 deletions(-)

diff --git a/test/test_run_difference_with_gpao.py b/test/test_run_difference_with_gpao.py
index 75804a2..7bb6614 100644
--- a/test/test_run_difference_with_gpao.py
+++ b/test/test_run_difference_with_gpao.py
@@ -40,11 +40,11 @@ def test_create_gpao_project():
 
 
 @pytest.mark.gpao
-def test_gpao_run():
+def test_gpao_run_with_stream():
     dtm_lidar_lhds = "./data/lhd_dir_gpao"
     output_dir = TMP_PATH / "gpao_run"
     output_dir.mkdir()
-    project_name = "test_run_altianalysis_gpao"
+    project_name = "test_run_altianalysis_gpao_stream"
 
     gpao_hostname = os.environ.get("GPAO_API_URL", "localhost")
     url_api = f"http://{gpao_hostname}:8080/api/"
@@ -59,3 +59,32 @@ def test_gpao_run():
     if gpao_hostname == "localhost":
         tu.execute_gpao_client(tags="docker", num_thread=4)
     wait_running_job(url_api, project_name, delay_second=1, delay_log_second=10)
+
+
+@pytest.mark.gpao
+def test_gpao_run_with_given_secondary_folder():
+    dtm_lidar_lhds = "./data/lhd_dir_gpao"
+    secondary_dtm_dir = "./data/lhd_dir_gpao"
+    output_dir = TMP_PATH / "gpao_run"
+    output_dir.mkdir()
+    project_name = "test_run_altianalysis_gpao_secondary_folder"
+
+    gpao_hostname = os.environ.get("GPAO_API_URL", "localhost")
+    url_api = f"http://{gpao_hostname}:8080/api/"
+
+    runner_store_path = Path(dtm_lidar_lhds).resolve()
+    local_store_path = Path("data/lhd_dir_gpao").resolve()
+
+    run_difference_with_gpao.compute_on_gpao(
+        Path(dtm_lidar_lhds),
+        Path(secondary_dtm_dir),
+        Path(output_dir),
+        gpao_hostname,
+        local_store_path,
+        runner_store_path,
+        project_name,
+    )
+
+    if gpao_hostname == "localhost":
+        tu.execute_gpao_client(tags="docker", num_thread=4)
+    wait_running_job(url_api, project_name, delay_second=1, delay_log_second=10)

From 321353770f3aa02d70bd7bdca1ce093839d734c8 Mon Sep 17 00:00:00 2001
From: DaliCHEBBI <mohamed-ali.chebbi@ign.fr>
Date: Thu, 25 Sep 2025 14:08:57 +0200
Subject: [PATCH 3/6] make some changes after review

---
 altianalysis/compute_difference.py           | 14 ++++++++++----
 altianalysis/run_difference_with_gpao.py     | 18 +++++++++++-------
 altianalysis/run_difference_with_parallel.py | 19 ++++++++++---------
 test/test_compute_difference.py              | 19 +++++++++++++------
 test/test_run_difference_with_gpao.py        |  4 ++--
 test/test_run_difference_with_parallel.py    | 11 ++++++++---
 6 files changed, 54 insertions(+), 31 deletions(-)

diff --git a/altianalysis/compute_difference.py b/altianalysis/compute_difference.py
index 60e41ac..01b5ed3 100644
--- a/altianalysis/compute_difference.py
+++ b/altianalysis/compute_difference.py
@@ -11,10 +11,16 @@
 
 
 def parse_args():
-    parser = argparse.ArgumentParser("compute difference map between lidar dtm and rge alti")
-    parser.add_argument("--dtm_lidar_file", type=str, help="dtm lidar tif file")
+    parser = argparse.ArgumentParser(
+        "compute difference between two elevation files or between one elevation file and rge alti"
+    )
+    parser.add_argument("--primary_elevation_file", type=str, help="dtm lidar tif file")
     parser.add_argument(
-        "--second_elevation_file", default=None, type=str, help="secondary elevation file when no stream to be used !"
+        "--second_elevation_file",
+        default=None,
+        type=str,
+        help="secondary elevation file to compare with primary elevation file. "
+        "If not provided, primary elevation file is compared with rge alti (1 meter) data stream",
     )
     parser.add_argument("--name_save_out", type=str, help="name of difference file")
     return parser.parse_args()
@@ -113,4 +119,4 @@ def main(reference_dtm_file: Path | str, secondary_dtm_file: Path | str | None,
 
 if __name__ == "__main__":
     args = parse_args()
-    main(args.dtm_lidar_file, args.second_elevation_file, args.name_save_out)
+    main(args.primary_elevation_file, args.second_elevation_file, args.name_save_out)
diff --git a/altianalysis/run_difference_with_gpao.py b/altianalysis/run_difference_with_gpao.py
index 62b4573..05ad338 100644
--- a/altianalysis/run_difference_with_gpao.py
+++ b/altianalysis/run_difference_with_gpao.py
@@ -1,5 +1,6 @@
 import argparse
 import logging
+import os
 from pathlib import Path, PurePosixPath
 from typing import List
 
@@ -27,26 +28,28 @@ def get_tile_names(folder: Path) -> List[str]:
 
 def create_one_job_one_difference(store: Store, dir_in: Path, second_dir: Path | None, input_file: str, output: Path):
     job_name = f"difference_{input_file}"
-    if second_dir is not None:
+    if second_dir:
+        secondary_file = second_dir / input_file
+        assert os.path.exists(secondary_file), "Secondary elevation does not exist to compute difference !"
         command = f"""
-    docker run -t --rm --userns=host --shm-size=2gb
+    docker run -t --rm --userns=host
     -v {store.to_unix(dir_in)}:/input
     -v {store.to_unix(second_dir)}:/second_input
     -v {store.to_unix(output)}:/output
     ghcr.io/ignf/altianalysis:{__version__}
     python -m altianalysis.compute_difference
-    --dtm_lidar_file /input/{input_file}
+    --primary_elevation_file /input/{input_file}
     --second_elevation_file /second_input/{input_file}
     --name_save_out /output/{input_file}
     """
     else:
         command = f"""
-    docker run -t --rm --userns=host --shm-size=2gb
+    docker run -t --rm --userns=host
     -v {store.to_unix(dir_in)}:/input
     -v {store.to_unix(output)}:/output
     ghcr.io/ignf/altianalysis:{__version__}
     python -m altianalysis.compute_difference
-    --dtm_lidar_file /input/{input_file}
+    --primary_elevation_file /input/{input_file}
     --name_save_out /output/{input_file}
     """
     job = Job(job_name, command, tags=["docker"])
@@ -181,11 +184,12 @@ def parse_args():
         help="Dossier des dalles MNT Lidar HD",
     )
     parser.add_argument(
-        "-i",
+        "-ii",
         "--secondary_dtm_dir",
         type=Path,
         default=None,
-        help="Dossier du second des MNT pour calculer la différence",
+        help="Dossier contenant le second ensemble de dalles MNT pour le calcul de différence. "
+        "Les dalles d'élévation doivent avoir les mêmes noms pour faire l'appariement",
     )
 
     parser.add_argument(
diff --git a/altianalysis/run_difference_with_parallel.py b/altianalysis/run_difference_with_parallel.py
index 8ba2df1..af25eb1 100644
--- a/altianalysis/run_difference_with_parallel.py
+++ b/altianalysis/run_difference_with_parallel.py
@@ -11,25 +11,25 @@ def _compute_one_difference(dtm_lhd_file: str, _dir: Path, _out_dir_difference:
 
     full_dtm_file = os.path.join(_dir, dtm_lhd_file)
     full_difference_file = os.path.join(_out_dir_difference, dtm_lhd_file)
-    _second_file = None
+    second_file = None
 
-    if second_dir is not None:
-        _second_file = os.path.join(second_dir, dtm_lhd_file)
+    if second_dir:
+        second_file = os.path.join(second_dir, dtm_lhd_file)
 
-    main(full_dtm_file, _second_file, full_difference_file)
+    main(full_dtm_file, second_file, full_difference_file)
 
 
-def compute_all_difference_maps(_dir: Path, _second_dir: Path | None, _out_dir_difference: Path):
+def compute_all_difference_maps(dir: Path, second_dir: Path | None, out_dir_difference: Path):
 
-    os.makedirs(_out_dir_difference, exist_ok=True)
+    os.makedirs(out_dir_difference, exist_ok=True)
     all_dtm_lhd_names = []
-    for dtm_file in _dir.iterdir():
+    for dtm_file in dir.iterdir():
         if dtm_file.is_file() and (str(dtm_file).endswith(".tif") or str(dtm_file).endswith(".TIF")):
             all_dtm_lhd_names.append(dtm_file.name)
 
     # bulk compute
     _ = Parallel(n_jobs=12, verbose=True)(
-        delayed(_compute_one_difference)(dtm_lhd_file, _dir, _out_dir_difference, second_dir=_second_dir)
+        delayed(_compute_one_difference)(dtm_lhd_file, dir, out_dir_difference, second_dir=second_dir)
         for dtm_lhd_file in all_dtm_lhd_names
     )
 
@@ -49,7 +49,8 @@ def parse_args():
         "--secondary_dtm_elevation_dir",
         type=Path,
         default=None,
-        help="Dossier contenant le second ensemble de dalles MNT pour le calcul de différence",
+        help="Dossier contenant le second ensemble de dalles MNT pour le calcul de différence. "
+        "Les dalles d'élévation doivent avoir les mêmes noms pour faire l'appariement",
     )
 
     parser.add_argument(
diff --git a/test/test_compute_difference.py b/test/test_compute_difference.py
index f4c041f..3dc0c1c 100644
--- a/test/test_compute_difference.py
+++ b/test/test_compute_difference.py
@@ -161,20 +161,27 @@ def test_compute_difference_with_nodata():
         assert np.all(nodata_diff_mask[:, :-1, :-1] == nodata_combined), "Added or missed nodata values !"
 
 
-def test_main():
-    output_dir = TMP_PATH / "main"
+def test_main_with_stream():
+    output_dir = TMP_PATH / "main_with_stream"
     output_dir.mkdir()
     dtm_lidar_file = "./data/lhd/Semis_2021_0886_6443_LA93_IGN69_50CM.tif"
 
-    second_dtm_file = "./data/lhd/Semis_2021_0886_6443_LA93_IGN69_50CM.tif"
-
     out_difference_file = output_dir / "Difference_with_rge_Semis_2021_0886_6443_LA93_IGN69_50CM.tif"
-    out_difference_file_with_self = output_dir / "Difference_self_with_rge_Semis_2021_0886_6443_LA93_IGN69_50CM.tif"
 
     compute_difference.main(dtm_lidar_file, None, out_difference_file)
 
     assert os.path.exists(out_difference_file), "difference with rge alti not computed !"
 
+
+def test_main_with_secondary_folder():
+    output_dir = TMP_PATH / "main_with_secondary_folder"
+    output_dir.mkdir()
+    dtm_lidar_file = "./data/lhd/Semis_2021_0886_6443_LA93_IGN69_50CM.tif"
+
+    second_dtm_file = "./data/lhd/Semis_2021_0886_6443_LA93_IGN69_50CM.tif"
+
+    out_difference_file_with_self = output_dir / "Difference_self_with_rge_Semis_2021_0886_6443_LA93_IGN69_50CM.tif"
+
     # run with secondary file
     compute_difference.main(dtm_lidar_file, second_dtm_file, out_difference_file_with_self)
 
@@ -182,4 +189,4 @@ def test_main():
 
     with rasterio.open(out_difference_file_with_self) as o_diff_self:
         diff = o_diff_self.read()
-        assert np.all(diff == 0), "difference with self yields null values"
+        assert np.all(diff == 0), "difference with self yields non null values"
diff --git a/test/test_run_difference_with_gpao.py b/test/test_run_difference_with_gpao.py
index a6eac39..cca2741 100644
--- a/test/test_run_difference_with_gpao.py
+++ b/test/test_run_difference_with_gpao.py
@@ -65,7 +65,7 @@ def test_create_gpao_projects_without_cog():
 @pytest.mark.gpao
 def test_gpao_run_with_cog_stream_rge():
     dtm_lidar_lhds = "./data/lhd_dir_gpao"
-    output_dir = TMP_PATH / "gpao_run_with_cog"
+    output_dir = TMP_PATH / "gpao_run_with_cog_stream_rge"
     output_dir.mkdir()
     cog_filename = "cog.tif"
     project_name = "test_run_altianalysis_gpao"
@@ -124,7 +124,7 @@ def test_gpao_run_without_cog_stream_rge():
 def test_gpao_run_without_cog_given_secondary_folder():
     dtm_lidar_lhds = "./data/lhd_dir_gpao"
     secondary_dtm_dir = "./data/lhd_dir_gpao"
-    output_dir = TMP_PATH / "gpao_run"
+    output_dir = TMP_PATH / "gpao_run_without_cog_given_secondary_folder"
     output_dir.mkdir()
     project_name = "test_run_altianalysis_gpao_secondary_folder"
 
diff --git a/test/test_run_difference_with_parallel.py b/test/test_run_difference_with_parallel.py
index f1746ad..bf2ecaa 100644
--- a/test/test_run_difference_with_parallel.py
+++ b/test/test_run_difference_with_parallel.py
@@ -15,8 +15,8 @@ def setup_module(module):
     os.makedirs(TMP_PATH)
 
 
-def test_compute_all_difference_maps():
-    output_dir = TMP_PATH / "compute_all_difference_maps"
+def test_compute_all_difference_maps_with_stream():
+    output_dir = TMP_PATH / "compute_all_difference_maps_with_stream"
     output_dir.mkdir()
     dtm_lidar_dir = Path("./data/lhd_dir_gpao")
 
@@ -31,8 +31,13 @@ def test_compute_all_difference_maps():
                 lidar_dtm_file
             )
 
+
+def test_compute_all_difference_maps_with_secondary_folder():
     # second test with secondary folder of dtm files holding the same names
-    output_dir_with_sec = TMP_PATH / "compute_all_difference_maps"
+    output_dir_with_sec = TMP_PATH / "compute_all_difference_maps_with_secondary_folder"
+    output_dir_with_sec.mkdir()
+
+    dtm_lidar_dir = Path("./data/lhd_dir_gpao")
     sec_dtm_dir = Path("./data/lhd_dir_gpao")
 
     run_difference_with_parallel.compute_all_difference_maps(dtm_lidar_dir, sec_dtm_dir, output_dir_with_sec)

From d02b8d47dd96639f790f30523fddf73ee0ce6edd Mon Sep 17 00:00:00 2001
From: DaliCHEBBI <mohamed-ali.chebbi@ign.fr>
Date: Thu, 25 Sep 2025 17:27:36 +0200
Subject: [PATCH 4/6] generic naming of input files

---
 altianalysis/compute_difference.py           | 32 ++++++++++----------
 altianalysis/run_difference_with_gpao.py     | 28 +++++++++--------
 altianalysis/run_difference_with_parallel.py | 22 +++++++-------
 3 files changed, 42 insertions(+), 40 deletions(-)

diff --git a/altianalysis/compute_difference.py b/altianalysis/compute_difference.py
index 01b5ed3..76b9d9d 100644
--- a/altianalysis/compute_difference.py
+++ b/altianalysis/compute_difference.py
@@ -14,7 +14,7 @@ def parse_args():
     parser = argparse.ArgumentParser(
         "compute difference between two elevation files or between one elevation file and rge alti"
     )
-    parser.add_argument("--primary_elevation_file", type=str, help="dtm lidar tif file")
+    parser.add_argument("--primary_elevation_file", type=str, help="primary elevation file")
     parser.add_argument(
         "--second_elevation_file",
         default=None,
@@ -27,7 +27,7 @@ def parse_args():
 
 
 def _extract_rge_alti_tile_from_stream(
-    dtm_lidar_file: str,
+    dtm_file: str,
     output_path: str | Path,
     stream_RGE="RGEALTI-MNT_PYR-ZIP_FXX_LAMB93_WMS",  # "ELEVATION.ELEVATIONGRIDCOVERAGE.HIGHRES",
     proj="2154",
@@ -37,7 +37,7 @@ def _extract_rge_alti_tile_from_stream(
 ):
 
     # compute dtm lidar extent while reading with rasterio
-    with rasterio.open(dtm_lidar_file) as dtm_lhd:
+    with rasterio.open(dtm_file) as dtm_lhd:
         bounds = dtm_lhd.bounds
         minx, miny, maxx, maxy = bounds.left, bounds.bottom, bounds.right, bounds.top
 
@@ -58,30 +58,30 @@ def _extract_rge_alti_tile_from_stream(
         return True
 
     except requests.exceptions.Timeout:
-        warnings.warn(f"Request time out for stream associated to {dtm_lidar_file}")
+        warnings.warn(f"Request time out for stream associated to {dtm_file}")
         return False
 
 
-def compute_difference_between_dtms(dtm_lidar_file: str, dtm_rge_tile: str, name_save_out: str) -> None:
+def compute_difference_between_dtms(first_dtm_file: str, second_dtm_file: str, name_save_out: str) -> None:
 
     # read dtm_lidar tile
-    with rasterio.open(dtm_lidar_file) as dtm_lidar, rasterio.open(dtm_rge_tile) as dtm_rge:
+    with rasterio.open(first_dtm_file) as dtm_1, rasterio.open(second_dtm_file) as dtm_2:
 
         # read dtm_lidar array
-        data_dtm_lidar = dtm_lidar.read(1)
+        data_dtm_1 = dtm_1.read(1)
 
         # copy metadata of mtd_lidar
-        meta_dtm_lidar = dtm_lidar.meta.copy()
+        meta_dtm_1 = dtm_1.meta.copy()
 
         # window from rge alti
-        window_rge = dtm_rge.window(*dtm_lidar.bounds)
+        window_2 = dtm_2.window(*dtm_1.bounds)
 
         # read the data from dtm_rge with the same window as dtm_lidar
-        data_dtm_rge_windowed = dtm_rge.read(
+        data_dtm_2_windowed = dtm_2.read(
             1,
-            window=window_rge,
+            window=window_2,
             boundless=True,
-            out_shape=data_dtm_lidar.shape,
+            out_shape=data_dtm_1.shape,
             resampling=Resampling.cubic,
             fill_value=0,
         )
@@ -89,14 +89,14 @@ def compute_difference_between_dtms(dtm_lidar_file: str, dtm_rge_tile: str, name
         # data_dtm_rge_windowed=np.where(data_dtm_rge_windowed==dtm_rge.nodata, 0,data_dtm_rge_windowed)
 
         # difference dem
-        _difference = data_dtm_lidar - data_dtm_rge_windowed
+        _difference = data_dtm_1 - data_dtm_2_windowed
 
-        _masq_nodata = np.logical_or((data_dtm_rge_windowed == dtm_rge.nodata), (data_dtm_lidar == dtm_lidar.nodata))
+        _masq_nodata = np.logical_or((data_dtm_2_windowed == dtm_2.nodata), (data_dtm_1 == dtm_1.nodata))
 
-        _difference[_masq_nodata] = dtm_lidar.nodata
+        _difference[_masq_nodata] = dtm_1.nodata
 
         # save result
-        with rasterio.open(name_save_out, "w", **meta_dtm_lidar) as dst:
+        with rasterio.open(name_save_out, "w", **meta_dtm_1) as dst:
             dst.write(_difference, 1)
 
 
diff --git a/altianalysis/run_difference_with_gpao.py b/altianalysis/run_difference_with_gpao.py
index 05ad338..00b4bc1 100644
--- a/altianalysis/run_difference_with_gpao.py
+++ b/altianalysis/run_difference_with_gpao.py
@@ -30,7 +30,10 @@ def create_one_job_one_difference(store: Store, dir_in: Path, second_dir: Path |
     job_name = f"difference_{input_file}"
     if second_dir:
         secondary_file = second_dir / input_file
-        assert os.path.exists(secondary_file), "Secondary elevation does not exist to compute difference !"
+
+        if not os.path.exists(secondary_file):
+            raise FileNotFoundError(f"Secondary elevation does not exist to compute difference for {input_file}")
+
         command = f"""
     docker run -t --rm --userns=host
     -v {store.to_unix(dir_in)}:/input
@@ -57,21 +60,21 @@ def create_one_job_one_difference(store: Store, dir_in: Path, second_dir: Path |
 
 
 def create_main_gpao_project(
-    dtms_lhd: Path,
+    primary_dir: Path,
     secondary_dir: Path | None,
     out: Path,
     store: Store,
     project_name: str,
 ) -> Project:
 
-    logging.debug(f"Create GPAO projects to compute difference maps with rge alti: {dtms_lhd}.")
+    logging.debug(f"Create GPAO projects to compute difference maps with rge alti: {primary_dir}.")
     logging.debug(f"Writing difference maps to {out}.")
 
     Project.reset()
 
     # get dtm tile names for lidar hd
 
-    dtm_tile_names = get_tile_names(dtms_lhd)
+    dtm_tile_names = get_tile_names(primary_dir)
 
     out.mkdir(parents=True, exist_ok=True)
 
@@ -80,7 +83,7 @@ def create_main_gpao_project(
     jobs = []
 
     for tile_ in dtm_tile_names:
-        job = create_one_job_one_difference(store, dtms_lhd, secondary_dir, tile_, out)
+        job = create_one_job_one_difference(store, primary_dir, secondary_dir, tile_, out)
         jobs.append(job)
 
     # create the project
@@ -120,9 +123,9 @@ def create_cog_gpao_project(
 
 
 def create_gpao_projects(
-    dtms_lhd: Path, secondary_dir: Path | None, out: Path, store: Store, project_name: str, cog_filename: str
+    primary_dir: Path, secondary_dir: Path | None, out: Path, store: Store, project_name: str, cog_filename: str
 ) -> List[Project]:
-    project_main = create_main_gpao_project(dtms_lhd, secondary_dir, out, store, project_name)
+    project_main = create_main_gpao_project(primary_dir, secondary_dir, out, store, project_name)
     projects = [project_main]
     if cog_filename:
         project_cog = create_cog_gpao_project(
@@ -134,7 +137,7 @@ def create_gpao_projects(
 
 
 def compute_on_gpao(
-    dtms_lhd: Path,
+    primary_dir: Path,
     secondary_dir: Path | None,
     out: Path,
     gpao_hostname: str,
@@ -163,7 +166,7 @@ def compute_on_gpao(
 
     logging.debug(f"Local store path ({local_store_path}) converted to client store path ({runner_store_path})")
 
-    projects = create_gpao_projects(dtms_lhd, secondary_dir, out, store, project_name, cog_filename)
+    projects = create_gpao_projects(primary_dir, secondary_dir, out, store, project_name, cog_filename)
 
     builder = Builder(projects)
 
@@ -177,11 +180,10 @@ def parse_args():
     parser = argparse.ArgumentParser(description="Calcul de cartes de différences par rapport au RGE ALTI")
     parser.add_argument(
         "-i",
-        "--dtm_lhd_dir",
+        "--primary_dtm_dir",
         type=Path,
-        # nargs="+",
         required=True,
-        help="Dossier des dalles MNT Lidar HD",
+        help="Dossier contenant le premier ensemble de dalles MNT pour le calcul de différence.",
     )
     parser.add_argument(
         "-ii",
@@ -234,7 +236,7 @@ def parse_args():
     args = parse_args()
 
     compute_on_gpao(
-        dtms_lhd=args.dtm_lhd_dir,
+        dtms_lhd=args.primary_dtm_dir,
         secondary_dir=args.secondary_dtm_dir,
         out=args.out,
         gpao_hostname=args.gpao_hostname,
diff --git a/altianalysis/run_difference_with_parallel.py b/altianalysis/run_difference_with_parallel.py
index af25eb1..386dd49 100644
--- a/altianalysis/run_difference_with_parallel.py
+++ b/altianalysis/run_difference_with_parallel.py
@@ -7,14 +7,14 @@
 from altianalysis.compute_difference import main
 
 
-def _compute_one_difference(dtm_lhd_file: str, _dir: Path, _out_dir_difference: Path, second_dir=None):
+def _compute_one_difference(dtm_file: str, _dir: Path, _out_dir_difference: Path, second_dir=None):
 
-    full_dtm_file = os.path.join(_dir, dtm_lhd_file)
-    full_difference_file = os.path.join(_out_dir_difference, dtm_lhd_file)
+    full_dtm_file = os.path.join(_dir, dtm_file)
+    full_difference_file = os.path.join(_out_dir_difference, dtm_file)
     second_file = None
 
     if second_dir:
-        second_file = os.path.join(second_dir, dtm_lhd_file)
+        second_file = os.path.join(second_dir, dtm_file)
 
     main(full_dtm_file, second_file, full_difference_file)
 
@@ -22,15 +22,15 @@ def _compute_one_difference(dtm_lhd_file: str, _dir: Path, _out_dir_difference:
 def compute_all_difference_maps(dir: Path, second_dir: Path | None, out_dir_difference: Path):
 
     os.makedirs(out_dir_difference, exist_ok=True)
-    all_dtm_lhd_names = []
+    all_dtm_names = []
     for dtm_file in dir.iterdir():
         if dtm_file.is_file() and (str(dtm_file).endswith(".tif") or str(dtm_file).endswith(".TIF")):
-            all_dtm_lhd_names.append(dtm_file.name)
+            all_dtm_names.append(dtm_file.name)
 
     # bulk compute
     _ = Parallel(n_jobs=12, verbose=True)(
-        delayed(_compute_one_difference)(dtm_lhd_file, dir, out_dir_difference, second_dir=second_dir)
-        for dtm_lhd_file in all_dtm_lhd_names
+        delayed(_compute_one_difference)(dtm_file, dir, out_dir_difference, second_dir=second_dir)
+        for dtm_file in all_dtm_names
     )
 
 
@@ -38,10 +38,10 @@ def parse_args():
     parser = argparse.ArgumentParser(description="Calcul de cartes de différences par rapport au RGE ALTI")
     parser.add_argument(
         "-l",
-        "--dtm_lidar_dir",
+        "--primary_dtm_dir",
         type=Path,
         required=True,
-        help="Dossier des dalles MNT Lidar HD",
+        help="Dossier contenant le premier ensemble de dalles MNT pour le calcul de différence.",
     )
 
     parser.add_argument(
@@ -66,4 +66,4 @@ def parse_args():
 
 if __name__ == "__main__":
     args = parse_args()
-    compute_all_difference_maps(args.dtm_lidar_dir, args.secondary_dtm_elevation_dir, args.name_dir_difference)
+    compute_all_difference_maps(args.primary_dtm_dir, args.secondary_dtm_elevation_dir, args.name_dir_difference)

From 1c818dca3ae3f3d954dbd5394c5b743b2f5e5e19 Mon Sep 17 00:00:00 2001
From: DaliCHEBBI <mohamed-ali.chebbi@ign.fr>
Date: Mon, 29 Sep 2025 10:15:36 +0200
Subject: [PATCH 5/6] compile change requests

---
 altianalysis/compute_difference.py           |  4 +-
 altianalysis/run_difference_with_gpao.py     | 41 ++++++++++++--------
 altianalysis/run_difference_with_parallel.py |  7 ++--
 3 files changed, 31 insertions(+), 21 deletions(-)

diff --git a/altianalysis/compute_difference.py b/altianalysis/compute_difference.py
index 76b9d9d..ceccab4 100644
--- a/altianalysis/compute_difference.py
+++ b/altianalysis/compute_difference.py
@@ -37,8 +37,8 @@ def _extract_rge_alti_tile_from_stream(
 ):
 
     # compute dtm lidar extent while reading with rasterio
-    with rasterio.open(dtm_file) as dtm_lhd:
-        bounds = dtm_lhd.bounds
+    with rasterio.open(dtm_file) as dtm:
+        bounds = dtm.bounds
         minx, miny, maxx, maxy = bounds.left, bounds.bottom, bounds.right, bounds.top
 
     try:
diff --git a/altianalysis/run_difference_with_gpao.py b/altianalysis/run_difference_with_gpao.py
index 00b4bc1..1074187 100644
--- a/altianalysis/run_difference_with_gpao.py
+++ b/altianalysis/run_difference_with_gpao.py
@@ -34,27 +34,26 @@ def create_one_job_one_difference(store: Store, dir_in: Path, second_dir: Path |
         if not os.path.exists(secondary_file):
             raise FileNotFoundError(f"Secondary elevation does not exist to compute difference for {input_file}")
 
-        command = f"""
-    docker run -t --rm --userns=host
-    -v {store.to_unix(dir_in)}:/input
-    -v {store.to_unix(second_dir)}:/second_input
-    -v {store.to_unix(output)}:/output
-    ghcr.io/ignf/altianalysis:{__version__}
-    python -m altianalysis.compute_difference
-    --primary_elevation_file /input/{input_file}
-    --second_elevation_file /second_input/{input_file}
-    --name_save_out /output/{input_file}
-    """
+        second_input_mount = f" -v {store.to_unix(second_dir)}:/second_input"
+        second_input_param = f"--second_elevation_file /second_input/{input_file}"
+
     else:
-        command = f"""
+
+        second_input_mount = ""
+        second_input_param = ""
+
+    command = f"""
     docker run -t --rm --userns=host
     -v {store.to_unix(dir_in)}:/input
+    {second_input_mount}
     -v {store.to_unix(output)}:/output
     ghcr.io/ignf/altianalysis:{__version__}
     python -m altianalysis.compute_difference
     --primary_elevation_file /input/{input_file}
+    {second_input_param}
     --name_save_out /output/{input_file}
     """
+
     job = Job(job_name, command, tags=["docker"])
     return job
 
@@ -67,7 +66,13 @@ def create_main_gpao_project(
     project_name: str,
 ) -> Project:
 
-    logging.debug(f"Create GPAO projects to compute difference maps with rge alti: {primary_dir}.")
+    if secondary_dir:
+        logging.debug(
+            f"Create GPAO projects to compute difference maps file by file between : \
+            {primary_dir} and {secondary_dir}.Note that files are matched by names."
+        )
+    else:
+        logging.debug(f"Create GPAO projects to compute difference maps with rge alti: {primary_dir}.")
     logging.debug(f"Writing difference maps to {out}.")
 
     Project.reset()
@@ -177,7 +182,10 @@ def compute_on_gpao(
 
 
 def parse_args():
-    parser = argparse.ArgumentParser(description="Calcul de cartes de différences par rapport au RGE ALTI")
+    parser = argparse.ArgumentParser(
+        description="Calcul de cartes de différences entre 2 sources de modèles numériques, "
+        "ou d'une source par rapport au RGE ALTI"
+    )
     parser.add_argument(
         "-i",
         "--primary_dtm_dir",
@@ -191,7 +199,8 @@ def parse_args():
         type=Path,
         default=None,
         help="Dossier contenant le second ensemble de dalles MNT pour le calcul de différence. "
-        "Les dalles d'élévation doivent avoir les mêmes noms pour faire l'appariement",
+        "Les dalles d'élévation doivent avoir les mêmes noms pour faire l'appariement"
+        "S'il est laissé vide, les dalles du premier ensemble sont comparées au RGE Alti",
     )
 
     parser.add_argument(
@@ -236,7 +245,7 @@ def parse_args():
     args = parse_args()
 
     compute_on_gpao(
-        dtms_lhd=args.primary_dtm_dir,
+        primary_dir=args.primary_dtm_dir,
         secondary_dir=args.secondary_dtm_dir,
         out=args.out,
         gpao_hostname=args.gpao_hostname,
diff --git a/altianalysis/run_difference_with_parallel.py b/altianalysis/run_difference_with_parallel.py
index 386dd49..fe0a0ef 100644
--- a/altianalysis/run_difference_with_parallel.py
+++ b/altianalysis/run_difference_with_parallel.py
@@ -46,11 +46,12 @@ def parse_args():
 
     parser.add_argument(
         "-s",
-        "--secondary_dtm_elevation_dir",
+        "--secondary_dtm_dir",
         type=Path,
         default=None,
         help="Dossier contenant le second ensemble de dalles MNT pour le calcul de différence. "
-        "Les dalles d'élévation doivent avoir les mêmes noms pour faire l'appariement",
+        "Les dalles d'élévation doivent avoir les mêmes noms pour faire l'appariement"
+        "S'il est laissé vide, les dalles du premier ensemble sont comparées au RGE Alti",
     )
 
     parser.add_argument(
@@ -66,4 +67,4 @@ def parse_args():
 
 if __name__ == "__main__":
     args = parse_args()
-    compute_all_difference_maps(args.primary_dtm_dir, args.secondary_dtm_elevation_dir, args.name_dir_difference)
+    compute_all_difference_maps(args.primary_dtm_dir, args.secondary_dtm_dir, args.name_dir_difference)

From 2d5a1e89e5d4a988159cecb9e60d1f6f9cb07afb Mon Sep 17 00:00:00 2001
From: DaliCHEBBI <mohamed-ali.chebbi@ign.fr>
Date: Mon, 29 Sep 2025 11:27:22 +0200
Subject: [PATCH 6/6] compile change requests

---
 altianalysis/run_difference_with_gpao.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/altianalysis/run_difference_with_gpao.py b/altianalysis/run_difference_with_gpao.py
index 1074187..08902c9 100644
--- a/altianalysis/run_difference_with_gpao.py
+++ b/altianalysis/run_difference_with_gpao.py
@@ -68,7 +68,7 @@ def create_main_gpao_project(
 
     if secondary_dir:
         logging.debug(
-            f"Create GPAO projects to compute difference maps file by file between : \
+            f"Create GPAO projects to compute difference maps file by file between: \
             {primary_dir} and {secondary_dir}.Note that files are matched by names."
         )
     else: