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Generalized specification of variable / coordinate / dimension units to templates. #714

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Merged
merged 12 commits into from
Oct 15, 2025
Merged

Generalized specification of variable / coordinate / dimension units to templates. #714

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ce626d4
update templates to use unit-aware metadata
tasansal Oct 14, 2025
ae40dc5
add spatial_dimension_names property to abstract_dataset_template and…
tasansal Oct 15, 2025
1aea091
update SEG-Y converter to include angle and spatial unit handling in …
tasansal Oct 15, 2025
2b97346
remove debug print statement from SEG-Y converter
tasansal Oct 15, 2025
7507222
update test_segy_spec_validation to use spatial_dimension_names and c…
tasansal Oct 15, 2025
5cd031e
replace `_get_unit` with `get_unit_by_key` across templates for consi…
tasansal Oct 15, 2025
33e862b
update SEG-Y converter to replace `horizontal_coordinate_scalar` with…
tasansal Oct 15, 2025
582e9fc
update quickstart tutorial to clarify unit handling and add examples …
tasansal Oct 15, 2025
f8151cd
update quickstart tutorial to use TimeUnitModel for specifying time u…
tasansal Oct 15, 2025
66487db
fix broken link in quickstart tutorial for "Fixing X/Y Units Issues" …
tasansal Oct 15, 2025
7599697
fix link anchor in quickstart tutorial for "Fixing X/Y Units Issues" …
tasansal Oct 15, 2025
f748adb
fix external link in quickstart tutorial for "Fixing X/Y Units Issues…
tasansal Oct 15, 2025
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110 changes: 58 additions & 52 deletions docs/tutorials/quickstart.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -46,10 +46,10 @@
]
},
{
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import os\n",
"\n",
Expand All @@ -75,6 +75,8 @@
"\n",
"MDIO uses [TGSAI/segy][segy-github] to parse the SEG-Y; the field names conform to its canonical keys defined in [SEGY Binary Header Keys][segy-binary-keys] and [SEGY Trace Header Keys][segy-trace-keys]. Since MDIO v1 we also introduced templates for common seismic data types. For instance, we will be using the `PostStack3DTime` template [here][mdio-template-poststack3dtime], which expects the same canonical keys.\n",
"\n",
"We will also specify the units for the time domain. The spatial units will be automatically parsed from SEG-Y binary header. However, there may be a case where it is corrupt in the file, for that see the [Fixing X/Y Units Issues](https://mdio-python.readthedocs.io/en/stable/tutorials/corrupt_files.html#fixing-x-y-units-issues) section.\n",
"\n",
"In summary, we will use the byte locations as defined for ingestion.\n",
"\n",
"[segy-github]: https://github.com/TGSAI/segy\n",
Expand All @@ -85,17 +87,20 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"import matplotlib.pyplot as plt\n",
"from segy.schema import HeaderField\n",
"from segy.standards import get_segy_standard\n",
"\n",
"from mdio import segy_to_mdio\n",
"from mdio.builder.schemas.v1.units import TimeUnitModel\n",
"from mdio.builder.template_registry import get_template\n",
"\n",
"teapot_trace_headers = [\n",
Expand All @@ -109,16 +114,17 @@
"teapot_segy_spec = rev0_segy_spec.customize(trace_header_fields=teapot_trace_headers)\n",
"\n",
"mdio_template = get_template(\"PostStack3DTime\")\n",
"unit_ms = TimeUnitModel(time=\"ms\")\n",
"mdio_template.add_units({\"time\": unit_ms})\n",
"\n",
"segy_to_mdio(\n",
" input_path=input_url,\n",
" output_path=\"filt_mig.mdio\",\n",
" segy_spec=teapot_segy_spec,\n",
" mdio_template=mdio_template,\n",
" overwrite=True,\n",
")"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "markdown",
Expand All @@ -141,19 +147,19 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"from mdio import open_mdio\n",
"\n",
"dataset = open_mdio(\"filt_mig.mdio\")\n",
"dataset"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "markdown",
Expand All @@ -170,16 +176,16 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"print(dataset[\"segy_file_header\"].attrs[\"textHeader\"])"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "markdown",
Expand All @@ -194,16 +200,16 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"dataset[\"segy_file_header\"].attrs[\"binaryHeader\"]"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "markdown",
Expand All @@ -221,42 +227,42 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"dataset.sizes"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"dataset.inline"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"dataset.crossline"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "markdown",
Expand All @@ -278,11 +284,13 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"from mdio.builder.schemas.v1.stats import SummaryStatistics\n",
"\n",
Expand All @@ -292,9 +300,7 @@
"il_dataset = dataset.sel(inline=278)\n",
"il_amp = il_dataset[\"amplitude\"].T\n",
"il_amp.plot(vmin=-2 * std, vmax=2 * std, cmap=\"gray_r\", yincrease=False);"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "markdown",
Expand All @@ -313,13 +319,13 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"twt_data = dataset[\"amplitude\"].sel(time=1000)\n",
"twt_data.plot(vmin=-2 * std, vmax=2 * std, cmap=\"gray_r\", x=\"cdp_x\", y=\"cdp_y\");"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "markdown",
Expand All @@ -336,19 +342,19 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"trace_mask = dataset.trace_mask[:]\n",
"\n",
"twt_data.plot(vmin=-2 * std, vmax=2 * std, cmap=\"gray_r\", x=\"cdp_x\", y=\"cdp_y\", alpha=0.5, figsize=(8, 5))\n",
"trace_mask.plot(vmin=0, vmax=1, x=\"cdp_x\", y=\"cdp_y\", alpha=0.5);"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "markdown",
Expand Down Expand Up @@ -380,29 +386,29 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"dataset.headers[\"cdp_x\"].compute()"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"dataset.headers[\"cdp_y\"].compute()"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "markdown",
Expand All @@ -423,11 +429,13 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"xl_dataset = dataset.sel(crossline=100) # slices everything available in MDIO dataset!\n",
"\n",
Expand All @@ -447,9 +455,7 @@
"hdr_ax.set_xlabel(\"\")\n",
"\n",
"plt.tight_layout()"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "markdown",
Expand All @@ -470,11 +476,13 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"from mdio import mdio_to_segy\n",
"\n",
Expand All @@ -483,9 +491,7 @@
" output_path=\"filt_mig_roundtrip.sgy\",\n",
" segy_spec=teapot_segy_spec,\n",
")"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "markdown",
Expand All @@ -511,11 +517,13 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"import numpy as np\n",
"from segy import SegyFile\n",
Expand All @@ -536,22 +544,17 @@
" np.testing.assert_equal(original_segy.trace[idx], roundtrip_segy.trace[idx])\n",
"\n",
"print(\"Files identical!\")"
],
"outputs": [],
"execution_count": null
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"source": [],
"outputs": [],
"execution_count": null
"source": []
}
],
"metadata": {
"mystnb": {
"execution_mode": "force"
},
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
Expand All @@ -569,6 +572,9 @@
"pygments_lexer": "ipython3",
"version": "3.13.5"
},
"mystnb": {
"execution_mode": "force"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {
Expand Down
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