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Merged
belletva merged 37 commits into from
Mar 5, 2026
Merged

CLI improvement #906

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ee17b56
add: test prepa data
marinebcht Jan 16, 2026
c34a956
add: possible output file for --template-config
marinebcht Jan 21, 2026
bea7b8d
change: --template-config template_config.yaml @cli argv
marinebcht Jan 22, 2026
f7bd448
fix: doc presentation + com null/None
marinebcht Jan 26, 2026
cf25770
fix: review Romain
marinebcht Jan 27, 2026
cc27d8a
fix: scale before/after + empty fig
marinebcht Jan 30, 2026
ebb1690
fix: table stats in accuracy
marinebcht Feb 4, 2026
07f404f
fix: table start
marinebcht Feb 5, 2026
65f5156
prop: cropp in html
marinebcht Feb 6, 2026
196f5ea
add: same scale intermediate plots
marinebcht Feb 9, 2026
dc8410f
fix: simplication vmin/vmax
marinebcht Feb 9, 2026
18092c7
fix: some opti
marinebcht Feb 9, 2026
a7084e1
fix: preprocessed data
marinebcht Feb 9, 2026
05b53f8
fix: same scale plot everywhere
marinebcht Feb 12, 2026
9e3d9cc
fix: css style
marinebcht Feb 12, 2026
a4517fe
fix: coord_intersection
marinebcht Feb 16, 2026
9591251
little fix
marinebcht Feb 16, 2026
399ec7b
fix: secure double plot
marinebcht Feb 16, 2026
1e11df1
fix: error from --template-config
marinebcht Feb 17, 2026
4bc1c81
fix: reviews: romain + valentine
marinebcht Feb 18, 2026
2a7dc39
fix: name in case of no coreg
marinebcht Feb 18, 2026
1391327
add: doc + unit change
marinebcht Feb 19, 2026
a6a30bf
fix: report error ?
marinebcht Feb 19, 2026
a7a0a0a
add: #854 issue points: html plot size + doc + add mask section
marinebcht Feb 23, 2026
026eca2
fixes: tests (files)
marinebcht Feb 23, 2026
f5a7a5e
fix: std/STD + format_values_stats + WIP mask
marinebcht Feb 24, 2026
a270b8f
fix: masks application
marinebcht Feb 24, 2026
029d498
fix: doc
marinebcht Feb 24, 2026
a5ab34d
fix: mask management in accuracy + test
marinebcht Feb 25, 2026
4848da3
fix: long same stats
marinebcht Feb 25, 2026
fab830e
fix: stats masks topo
marinebcht Feb 26, 2026
1c23ab9
fix: doc ci
marinebcht Feb 26, 2026
33acad1
add: default cmap
marinebcht Mar 2, 2026
7d955f5
fix: test on masks + mask handle when only one is given + test std/STD
marinebcht Mar 3, 2026
7aad6cd
Default stats list reduction
marinebcht Mar 4, 2026
20c5e41
fix: test plot masked data
marinebcht Mar 4, 2026
d0bce9d
fix: LZD even for the tests
marinebcht Mar 4, 2026
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56 changes: 15 additions & 41 deletions doc/source/_workflows/outputs_accuracy/report.html
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Expand Up @@ -2,11 +2,10 @@
<head><meta charset='UTF-8'><title>Qualify elevation results</title></head>
<body>
<h1>Accuracy assessment report — xDEM</h1>
<p>xDEM version: 0.1.dev729</p><p>Date: 13/01/2026 15:02:39</p><p>Computing time: 23.89 seconds</p><h2>Elevation datasets</h2>
<div style='display: flex; gap: 10px;'>
<img src='plots/reference_elev_map.png' alt='Image PNG' style='max-width: 50%; height: auto; width: 50%;'>
<img src='plots/to_be_aligned_elev_map.png' alt='Image PNG' style='max-width: 50%; height: auto; width: 50%;'>
</div>
<p>xDEM version: 0.2.3.dev26</p><p>Date: 04/03/2026 15:54:49</p><p>Computing time: 29.13 seconds</p><h2>Elevation inputs</h2>
<img src='plots/inputs.png' alt='Image PNG' style='width: 100%; height: auto;'>
<h2>Masked elevation data</h2>
<img src='plots/masked_elev_map.png' alt='Image PNG' style='width: 100%; height: auto;'>
<div style='clear: both; margin-bottom: 30px;'>
<h2>Information about inputs</h2>
<table border='1' cellspacing='0' cellpadding='5'>
Expand All @@ -16,6 +15,8 @@ <h2>Information about inputs</h2>
<tr><td>sampling_grid</td><td>reference_elev</td></tr>
</table>
</div>
<h2>Preprocessed elevation data</h2>
<img src='plots/preprocessed_to_be_aligned_elev_map.png' alt='Image PNG' style='width: 100%; height: auto;'>
<div style='clear: both; margin-bottom: 30px;'>
<h2>Coregistration user configuration</h2>
<table border='1' cellspacing='0' cellpadding='5'>
Expand Down Expand Up @@ -44,43 +45,16 @@ <h2>LZD outputs</h2>
</table>
</div>
<h2>Statistics</h2>
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th>Data</th>
<th>Median</th>
<th>NMAD</th>
<th>Valid count</th>
</tr>
</thead>
<tbody>
<tr>
<td>Aligned elevation</td>
<td>363.338928</td>
<td>291.801208</td>
<td>1309704</td>
</tr>
<tr>
<td>Difference before coreg</td>
<td>2.766407</td>
<td>3.805830</td>
<td>1312020</td>
</tr>
<tr>
<td>Difference after coreg</td>
<td>0.254444</td>
<td>2.403943</td>
<td>1309704</td>
</tr>
</tbody>
</table><h2>Elevation differences</h2>
<div style='display: flex; gap: 10px;'>
<img src='plots/diff_elev_before_coreg_map.png' alt='Image PNG' style='max-width: 50%; height: auto; width: 50%;'>
<img src='plots/diff_elev_after_coreg_map.png' alt='Image PNG' style='max-width: 50%; height: auto; width: 50%;'>
</div>
<table border='1' cellspacing='0' cellpadding='5'>
<tr><td style="font-weight:bold">Data</td><td style="font-weight:bold">Aligned elevation</td><td style="font-weight:bold">Difference before coreg</td><td style="font-weight:bold">Difference after coreg</td></tr>
<tr><td>Median</td><td>316.330</td><td>2.334</td><td>-0.048</td></tr>
<tr><td>NMAD</td><td>277.103</td><td>3.417</td><td>2.050</td></tr>
<tr><td>Valid count</td><td>1133607</td><td>1145221</td><td>1133607</td></tr>
</table>
<h2>Elevation differences</h2>
<img src='plots/diff_elev_diff_coreg_map.png' alt='Image PNG' style='width: 100%; height: auto'>
<h2>Differences histogram</h2>
<img src='plots/elev_diff_histo.png' alt='Image PNG' style='max-width: 100%; height: auto;'>
<img src='plots/elev_diff_histo.png' alt='Image PNG' style='width: 100%; height: auto'>

</div>
</body>
</html>
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25 changes: 8 additions & 17 deletions doc/source/_workflows/outputs_topo/report.html
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Expand Up @@ -2,10 +2,10 @@
<head><meta charset='UTF-8'><title>Topographic summary results</title></head>
<body>
<h1>Topography summary report — xDEM</h1>
<p>xDEM version: 0.1.dev729</p><p>Date: 13/01/2026 15:02:58</p><p>Computing time: 9.71 seconds</p><h2>Elevation data</h2>
<img src='plots/elev_map.png' alt='Image PNG' style='max-width: 100%; height: auto;'>
<p>xDEM version: 0.2.3.dev26</p><p>Date: 04/03/2026 15:55:14</p><p>Computing time: 16.52 seconds</p><h2>Elevation input</h2>
<img src='plots/elev_map.png' alt='Image PNG' style='width: 100%; height: auto;'>
<h2>Masked elevation data</h2>
<img src='plots/masked_elev_map.png' alt='Image PNG' style='max-width: 100%; height: auto;'>
<img src='plots/masked_elev_map.png' alt='Image PNG' style='width: 100%; height: auto;'>
<div style='clear: both; margin-bottom: 30px;'>
<h2>Information about inputs</h2>
<table border='1' cellspacing='0' cellpadding='5'>
Expand Down Expand Up @@ -34,24 +34,15 @@ <h2>Elevation information</h2>
</table>
</div>
<div style='clear: both; margin-bottom: 30px;'>
<h2>Global statistics</h2>
<h2>Statistics</h2>
<table border='1' cellspacing='0' cellpadding='5'>
<tr><th>Information</th><th>Value</th></tr>
<tr><td>median</td><td>360.65</td></tr>
<tr><td>nmad</td><td>290.22</td></tr>
<tr><td>validcount</td><td>1312020</td></tr>
</table>
</div>
<div style='clear: both; margin-bottom: 30px;'>
<h2>Mask statistics</h2>
<table border='1' cellspacing='0' cellpadding='5'>
<tr><th>Information</th><th>Value</th></tr>
<tr><td>median</td><td>318.29</td></tr>
<tr><td>nmad</td><td>278.1</td></tr>
<tr><td>validcount</td><td>1312020</td></tr>
<tr><td>Median</td><td>318.290</td></tr>
<tr><td>NMAD</td><td>278.100</td></tr>
<tr><td>Valid count</td><td>1145221</td></tr>
</table>
</div>
<h2>Terrain attributes</h2>
<img src='plots/terrain_attributes_map.png' alt='Image PNG' style='max-width: 100%; height: auto;'>
<img src='plots/terrain_attributes_map.png' alt='Image PNG' style='width: 100%; height: auto;'>
</body>
</html>
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37 changes: 5 additions & 32 deletions doc/source/cli_accuracy.md
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Expand Up @@ -116,13 +116,13 @@ These categories and detailed parameter values are further detailed below:

**Required:** Yes

Elevation input information, split between reference and to-be-aligned elevation data.
Inputs information, split between reference and to-be-aligned elevation data.

:::::{tab-set}
::::{tab-item} `reference_elev`
::::{tab-item} `reference_elev` / `to_be_aligned_elev`

:::{table} Inputs parameters for `reference_elev`
:widths: 20, 35, 17, 18, 10
:::{table} Inputs parameters for `reference_elev` and `to_be_aligned_elev`
:widths: 20, 40, 20, 10, 10

| Name | Description | Type | Default | Required |
|-----------------------|------------------------------------------|------------|---------|----------|
Expand All @@ -146,40 +146,13 @@ Please refer to {ref}`data-example` to have more information.

::::

::::{tab-item} `to_be_aligned_elev`

:::{table} Inputs parameters for `to_be_aligned_elev`
:widths: 20, 35, 17, 18, 10

| Name | Description | Type | Default | Required |
|------------------------|------------------------------------------|------------|----------|----------|
| `path_to_elev` | Path to to-be-aligned elevation | str | | Yes |
| `force_source_nodata` | No data elevation | int | | No |
| `path_to_mask` | Path to mask associated to the elevation | str | | No |
| `from_vcrs` | Original vcrs | int, str | `null` | No |
| `to_vcrs` | Destination vcrs | int, str | `null` | No |
| `downsample` | Downsampling elevation factor >= 1 | int, float | 1 | No |
:::

:::{note}
For transforming between vertical CRS with ``from_vcrs``/``to_vcrs`` please refer to {ref}`vertical-ref`.
The ``downsample`` parameter allows the user to resample the elevation by a round factor.
The default value of 1 means no downsampling.

And, if you want to test the CLI with xDEM example data, they can also refer to data alias.
Please refer to {ref}`data-example` to have more information.
:::



::::

::::{tab-item} `sampling_grid`

Raster to match for reprojection.

:::{table} Values for ``sampling_grid``
:widths: 30, 40, 10, 10, 10
:widths: 30, 60, 10

| Value | Description | Default |
|----------------------|-------------------------------------------------------------------------|---------|
Expand Down
20 changes: 2 additions & 18 deletions tests/test_workflows/conftest.py
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Expand Up @@ -25,7 +25,7 @@

import xdem
from xdem.workflows import Accuracy
from xdem.workflows.schemas import TERRAIN_ATTRIBUTES_DEFAULT
from xdem.workflows.schemas import MIN_STATS, TERRAIN_ATTRIBUTES_DEFAULT


@pytest.fixture()
Expand Down Expand Up @@ -114,23 +114,7 @@ def pipeline_topo():
"downsample": 1,
}
},
"statistics": [
"mean",
"median",
"max",
"min",
"sum",
"sumofsquares",
"90thpercentile",
"le90",
"nmad",
"rmse",
"std",
"standarddeviation",
"validcount",
"totalcount",
"percentagevalidpoints",
],
"statistics": MIN_STATS,
"terrain_attributes": TERRAIN_ATTRIBUTES_DEFAULT,
"outputs": {"path": "outputs", "level": 1},
}
Expand Down
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