sbpio 0.1.0__tar.gz

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Files changed (13) hide show
  1. sbpio-0.1.0/LICENSE +21 -0
  2. sbpio-0.1.0/PKG-INFO +199 -0
  3. sbpio-0.1.0/README.md +134 -0
  4. sbpio-0.1.0/pyproject.toml +103 -0
  5. sbpio-0.1.0/sbpio/__init__.py +87 -0
  6. sbpio-0.1.0/sbpio/core.py +1055 -0
  7. sbpio-0.1.0/sbpio/utils.py +732 -0
  8. sbpio-0.1.0/sbpio.egg-info/PKG-INFO +199 -0
  9. sbpio-0.1.0/sbpio.egg-info/SOURCES.txt +11 -0
  10. sbpio-0.1.0/sbpio.egg-info/dependency_links.txt +1 -0
  11. sbpio-0.1.0/sbpio.egg-info/requires.txt +19 -0
  12. sbpio-0.1.0/sbpio.egg-info/top_level.txt +1 -0
  13. sbpio-0.1.0/setup.cfg +4 -0
sbpio-0.1.0/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2024 Ali Mohamed
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
sbpio-0.1.0/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: sbpio
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+ Version: 0.1.0
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+ Summary: Sub-Bottom Profiler (SBP) seismic data I/O and processing toolkit
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+ Author-email: Ali Mohamed <aliarafa327@gmail.com>
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+ License: MIT License
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+
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+ Copyright (c) 2024 Ali Mohamed
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
12
+ in the Software without restriction, including without limitation the rights
13
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
14
+ copies of the Software, and to permit persons to whom the Software is
15
+ furnished to do so, subject to the following conditions:
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+
17
+ The above copyright notice and this permission notice shall be included in all
18
+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
21
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
22
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
23
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
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+
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+ Project-URL: Homepage, https://github.com/PG-Ali-E-Mohamed/sbpio
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+ Project-URL: Repository, https://github.com/PG-Ali-E-Mohamed/sbpio
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+ Project-URL: Issues, https://github.com/PG-Ali-E-Mohamed/sbpio/issues
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+ Project-URL: Changelog, https://github.com/PG-Ali-E-Mohamed/sbpio/blob/main/CHANGELOG.md
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+ Keywords: sub-bottom profiler,SBP,SEG-Y,marine geophysics,seismic processing,oceanography
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+ Classifier: Development Status :: 3 - Alpha
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: Python :: 3.8
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+ Classifier: Programming Language :: Python :: 3.9
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Operating System :: OS Independent
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+ Requires-Python: >=3.8
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ Requires-Dist: matplotlib>=3.3
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+ Requires-Dist: numpy>=1.20
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+ Requires-Dist: pandas>=1.3
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+ Requires-Dist: geopandas>=0.10
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+ Requires-Dist: segyio>=1.9
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+ Requires-Dist: tqdm>=4.50
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+ Requires-Dist: scikit-image>=0.2
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+ Requires-Dist: shapely>=1.8
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+ Requires-Dist: pyproj>=3.1
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+ Requires-Dist: scipy>=1.7
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+ Provides-Extra: dev
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+ Requires-Dist: pytest>=7.0; extra == "dev"
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+ Requires-Dist: pytest-cov>=3.0; extra == "dev"
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+ Requires-Dist: black>=22.0; extra == "dev"
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+ Requires-Dist: isort>=5.0; extra == "dev"
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+ Requires-Dist: flake8>=4.0; extra == "dev"
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+ Requires-Dist: build; extra == "dev"
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+ Requires-Dist: twine; extra == "dev"
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+ Dynamic: license-file
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+
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+ # sbpio
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+
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+ **Sub-Bottom Profiler I/O and Processing Toolkit**
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+
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+ A Python library for reading, processing, and writing sub-bottom profiler (SBP) data stored in SEG-Y format.
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+
72
+ ---
73
+
74
+ ## Features
75
+
76
+ - Load SEG-Y SBP files
77
+ - Apply duplicate-trace removal
78
+ - Apply time-varying gain (TVG) with built-in or custom functions
79
+ - Recording-delay time correction
80
+ - Water-column and multiple muting
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+ - Shot-point navigation extraction, reprojection, and shapefile export
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+ - Cropping in specific time and traces ranges or within ROI polygon
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+ - Coordinate reprojection (e.g., from arc seconds to UTM)
84
+ - One-shot `write_processed()` pipeline for batch export
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+
86
+ ---
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+
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+ ## Installation
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+
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+ ### From PyPI
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+
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+ ```bash
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+ pip install sbpio
94
+ ```
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+
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+ ### From GitHub
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+
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+ ```bash
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+ pip install git+https://github.com/PG-Ali-E-Mohamed/sbpio.git
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+ ```
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+
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+ ## Quick Start
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+
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+ ```python
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+ from sbpio import sbp
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+
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+ # Open a SEG-Y file
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+ data = sbp("profile.segy")
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+
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+ # Display the envelope attribute
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+ data.show()
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+
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+ # One-shot processing pipeline
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+ data.write_processed(
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+ "output.segy",
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+ correct_delay=True,
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+ tvg={"method": 3, "kwargs": {"n": 0.2}},
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+ recoverable_penetration=200,
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+ out_projection="EPSG:32618",
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+ )
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+ ```
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+
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+ ---
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+
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+ ## API Overview
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+
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+ ### `sbp` class
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+
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+ The main entry point.
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+
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+ | Method | Description |
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+ |---|---|
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+ | `sbp(fname)` | Open a SEG-Y file |
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+ | `.load()` | Load traces and optionally compute envelope |
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+ | `.show()` | Display the profile |
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+ | `.tvg_gain()` | Apply time-varying gain |
137
+ | `.correct_delay()` | Correct recording delay |
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+ | `.clean_water_column()` | Mute the water column |
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+ | `.clean_below_seafloor()` | Mute below seafloor + offset |
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+ | `.crop()` | Define a time/trace crop window |
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+ | `.write()` | Write to SEG-Y |
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+ | `.write_processed()` | Full pipeline in one call |
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+
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+ ### `nav` class
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+
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+ Accessed via `data.navs`.
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+
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+ | Method | Description |
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+ |---|---|
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+ | `.shot_points()` | Extract navigation from headers |
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+ | `.coords_2_utm()` | Reproject coordinates to UTM |
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+ | `.to_shp(outfile)` | Export to shapefile (line or points) |
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+
154
+ ### TVG methods
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+
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+ Three built-in gain functions are available via `tvg_gain(method=N)`:
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+
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+ | Key | Function | Formula |
159
+ |---|---|---|
160
+ | `1` | `power_gain_1` | `(a·t + b)^n` |
161
+ | `2` | `power_gain_2` | `t^n` |
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+ | `3` | `power_gain_3` | `(t/dt)^n` |
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+
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+ The default is `tv_gamma` — a time-varying gamma correction that progressively brightens sub-seafloor reflections.
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+
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+ Pass a custom callable with signature `f(t, traces, **kwargs)` for full control.
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+
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+ ---
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+
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+ ## SEG-Y Conventions
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+
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+ sbpio follows standard SEG-Y Rev 1 trace header fields:
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+
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+ | Field | Byte location |
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+ |---|---|
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+ | Source X | 73 |
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+ | Source Y | 77 |
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+ | SourceGroupScalar | 69 |
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+ | CoordinateUnits | 89 |
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+ | DelayRecordingTime | 109 |
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+ | SourceWaterDepth | 61 |
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+ | EnergySourcePoint | 17 |
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+
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+ ---
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+
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+ ## Dependencies
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+
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+ | Package | Purpose |
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+ |---|---|
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+ | `segyio` | SEG-Y read/write |
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+ | `numpy` | Array operations |
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+ | `pandas` | Tabular data (navigation) |
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+ | `geopandas` | Shapefile I/O |
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+ | `shapely` | Geometry operations |
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+ | `pyproj` | Coordinate reprojection |
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+ | `matplotlib` | Plotting |
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+ | `scikit-image` | Image enhancement and resize |
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+ | `tqdm` | Progress bars |
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+ | `scipy` | Interpolation/ Envelope calculation |
sbpio-0.1.0/README.md ADDED
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+ # sbpio
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+
3
+ **Sub-Bottom Profiler I/O and Processing Toolkit**
4
+
5
+ A Python library for reading, processing, and writing sub-bottom profiler (SBP) data stored in SEG-Y format.
6
+
7
+ ---
8
+
9
+ ## Features
10
+
11
+ - Load SEG-Y SBP files
12
+ - Apply duplicate-trace removal
13
+ - Apply time-varying gain (TVG) with built-in or custom functions
14
+ - Recording-delay time correction
15
+ - Water-column and multiple muting
16
+ - Shot-point navigation extraction, reprojection, and shapefile export
17
+ - Cropping in specific time and traces ranges or within ROI polygon
18
+ - Coordinate reprojection (e.g., from arc seconds to UTM)
19
+ - One-shot `write_processed()` pipeline for batch export
20
+
21
+ ---
22
+
23
+ ## Installation
24
+
25
+ ### From PyPI
26
+
27
+ ```bash
28
+ pip install sbpio
29
+ ```
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+
31
+ ### From GitHub
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+
33
+ ```bash
34
+ pip install git+https://github.com/PG-Ali-E-Mohamed/sbpio.git
35
+ ```
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+
37
+ ## Quick Start
38
+
39
+ ```python
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+ from sbpio import sbp
41
+
42
+ # Open a SEG-Y file
43
+ data = sbp("profile.segy")
44
+
45
+ # Display the envelope attribute
46
+ data.show()
47
+
48
+ # One-shot processing pipeline
49
+ data.write_processed(
50
+ "output.segy",
51
+ correct_delay=True,
52
+ tvg={"method": 3, "kwargs": {"n": 0.2}},
53
+ recoverable_penetration=200,
54
+ out_projection="EPSG:32618",
55
+ )
56
+ ```
57
+
58
+ ---
59
+
60
+ ## API Overview
61
+
62
+ ### `sbp` class
63
+
64
+ The main entry point.
65
+
66
+ | Method | Description |
67
+ |---|---|
68
+ | `sbp(fname)` | Open a SEG-Y file |
69
+ | `.load()` | Load traces and optionally compute envelope |
70
+ | `.show()` | Display the profile |
71
+ | `.tvg_gain()` | Apply time-varying gain |
72
+ | `.correct_delay()` | Correct recording delay |
73
+ | `.clean_water_column()` | Mute the water column |
74
+ | `.clean_below_seafloor()` | Mute below seafloor + offset |
75
+ | `.crop()` | Define a time/trace crop window |
76
+ | `.write()` | Write to SEG-Y |
77
+ | `.write_processed()` | Full pipeline in one call |
78
+
79
+ ### `nav` class
80
+
81
+ Accessed via `data.navs`.
82
+
83
+ | Method | Description |
84
+ |---|---|
85
+ | `.shot_points()` | Extract navigation from headers |
86
+ | `.coords_2_utm()` | Reproject coordinates to UTM |
87
+ | `.to_shp(outfile)` | Export to shapefile (line or points) |
88
+
89
+ ### TVG methods
90
+
91
+ Three built-in gain functions are available via `tvg_gain(method=N)`:
92
+
93
+ | Key | Function | Formula |
94
+ |---|---|---|
95
+ | `1` | `power_gain_1` | `(a·t + b)^n` |
96
+ | `2` | `power_gain_2` | `t^n` |
97
+ | `3` | `power_gain_3` | `(t/dt)^n` |
98
+
99
+ The default is `tv_gamma` — a time-varying gamma correction that progressively brightens sub-seafloor reflections.
100
+
101
+ Pass a custom callable with signature `f(t, traces, **kwargs)` for full control.
102
+
103
+ ---
104
+
105
+ ## SEG-Y Conventions
106
+
107
+ sbpio follows standard SEG-Y Rev 1 trace header fields:
108
+
109
+ | Field | Byte location |
110
+ |---|---|
111
+ | Source X | 73 |
112
+ | Source Y | 77 |
113
+ | SourceGroupScalar | 69 |
114
+ | CoordinateUnits | 89 |
115
+ | DelayRecordingTime | 109 |
116
+ | SourceWaterDepth | 61 |
117
+ | EnergySourcePoint | 17 |
118
+
119
+ ---
120
+
121
+ ## Dependencies
122
+
123
+ | Package | Purpose |
124
+ |---|---|
125
+ | `segyio` | SEG-Y read/write |
126
+ | `numpy` | Array operations |
127
+ | `pandas` | Tabular data (navigation) |
128
+ | `geopandas` | Shapefile I/O |
129
+ | `shapely` | Geometry operations |
130
+ | `pyproj` | Coordinate reprojection |
131
+ | `matplotlib` | Plotting |
132
+ | `scikit-image` | Image enhancement and resize |
133
+ | `tqdm` | Progress bars |
134
+ | `scipy` | Interpolation/ Envelope calculation |
sbpio-0.1.0/pyproject.toml ADDED
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+ [build-system]
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+ requires = ["setuptools>=64", "wheel"]
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+ build-backend = "setuptools.build_meta"
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+
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+ # ---------------------------------------------------------------------------
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+ # Project metadata (PEP 621)
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+ # ---------------------------------------------------------------------------
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+
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+ [project]
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+ name = "sbpio"
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+ version = "0.1.0"
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+ description = "Sub-Bottom Profiler (SBP) seismic data I/O and processing toolkit"
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+ readme = "README.md"
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+ license = { file = "LICENSE" }
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+ requires-python = ">=3.8"
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+ authors = [
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+ { name = "Ali Mohamed", email = "aliarafa327@gmail.com" },
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+ ]
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+ keywords = [
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+ "sub-bottom profiler",
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+ "SBP",
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+ "SEG-Y",
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+ "marine geophysics",
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+ "seismic processing",
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+ "oceanography",
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+ ]
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+ classifiers = [
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+ "Development Status :: 3 - Alpha",
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+ "Intended Audience :: Science/Research",
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+ "License :: OSI Approved :: MIT License",
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+ "Programming Language :: Python :: 3",
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+ "Programming Language :: Python :: 3.8",
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+ "Programming Language :: Python :: 3.9",
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+ "Programming Language :: Python :: 3.10",
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+ "Programming Language :: Python :: 3.11",
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+ "Programming Language :: Python :: 3.12",
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+ "Operating System :: OS Independent",
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+ ]
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+
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+ # ---------------------------------------------------------------------------
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+ # Runtime dependencies
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+ # ---------------------------------------------------------------------------
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+
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+ dependencies = [
45
+ "matplotlib>=3.3",
46
+ "numpy>=1.20",
47
+ "pandas>=1.3",
48
+ "geopandas>=0.10",
49
+ "segyio>=1.9",
50
+ "tqdm>=4.50",
51
+ "scikit-image>=0.2",
52
+ "shapely>=1.8",
53
+ "pyproj>=3.1",
54
+ "scipy>=1.7",
55
+ ]
56
+
57
+ # ---------------------------------------------------------------------------
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+ # Optional / development dependencies
59
+ # ---------------------------------------------------------------------------
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+
61
+ [project.optional-dependencies]
62
+ dev = [
63
+ "pytest>=7.0",
64
+ "pytest-cov>=3.0",
65
+ "black>=22.0",
66
+ "isort>=5.0",
67
+ "flake8>=4.0",
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+ "build",
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+ "twine",
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+ ]
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+
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+ # ---------------------------------------------------------------------------
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+ # URLs shown on PyPI
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+ # ---------------------------------------------------------------------------
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+
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+ [project.urls]
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+ Homepage = "https://github.com/PG-Ali-E-Mohamed/sbpio"
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+ Repository = "https://github.com/PG-Ali-E-Mohamed/sbpio"
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+ Issues = "https://github.com/PG-Ali-E-Mohamed/sbpio/issues"
80
+ Changelog = "https://github.com/PG-Ali-E-Mohamed/sbpio/blob/main/CHANGELOG.md"
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+
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+ # ---------------------------------------------------------------------------
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+ # Package discovery
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+ # ---------------------------------------------------------------------------
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+
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+ [tool.setuptools.packages.find]
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+ include = ["sbpio*"]
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+
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+ # ---------------------------------------------------------------------------
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+ # Tool configuration
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+ # ---------------------------------------------------------------------------
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+
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+ [tool.black]
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+ line-length = 88
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+ target-version = ["py38", "py39", "py310", "py311"]
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+
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+ [tool.isort]
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+ profile = "black"
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+
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+ [tool.pytest.ini_options]
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+ testpaths = ["tests"]
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+ addopts = "-v --tb=short"
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+ filterwarnings = ["ignore::DeprecationWarning"]
sbpio-0.1.0/sbpio/__init__.py ADDED
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1
+ """
2
+ sbpio — Sub-Bottom Profiler I/O and Processing Toolkit
3
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4
+
5
+ Read, process, and write sub-bottom profiler (SBP) seismic data
6
+ in SEG-Y format.
7
+
8
+ Quick start::
9
+
10
+ from sbpio import sbp
11
+
12
+ data = sbp("profile.segy")
13
+ data.show()
14
+
15
+ data.write_processed(
16
+ "output.segy",
17
+ correct_delay=True,
18
+ tvg={"method": 3, "kwargs": {"n": 0.2}},
19
+ recoverable_penetration=200,
20
+ out_projection="EPSG:32618",
21
+ )
22
+ """
23
+ import warnings
24
+ # This suppresses all warnings
25
+ warnings.filterwarnings("ignore")
26
+
27
+ from .core import nav, sbp
28
+ from .utils import (
29
+ apply_tvg,
30
+ clear_multiples,
31
+ clear_water,
32
+ decode_nav,
33
+ degrees_minutes_seconds_to_decimal_degrees,
34
+ enhance,
35
+ extract_seafloor,
36
+ find_line_polygon_intersection_indices,
37
+ get_delay_recording_time,
38
+ get_water_depth,
39
+ mfv_fltr,
40
+ non_duplicates,
41
+ plot_sec,
42
+ power_gain_1,
43
+ power_gain_2,
44
+ power_gain_3,
45
+ samples_after_delay,
46
+ scale_to_range,
47
+ tv_gamma,
48
+ utm_to_decimal_degrees,
49
+ water_depth_to_time,
50
+ )
51
+
52
+ __version__ = "0.1.0"
53
+ __author__ = "Ali Mohamed"
54
+ __license__ = "MIT"
55
+
56
+ __all__ = [
57
+ # Classes
58
+ "sbp",
59
+ "nav",
60
+ # Visualisation
61
+ "enhance",
62
+ "plot_sec",
63
+ # Navigation
64
+ "decode_nav",
65
+ "degrees_minutes_seconds_to_decimal_degrees",
66
+ "utm_to_decimal_degrees",
67
+ "find_line_polygon_intersection_indices",
68
+ # SEG-Y helpers
69
+ "samples_after_delay",
70
+ "get_delay_recording_time",
71
+ "get_water_depth",
72
+ "non_duplicates",
73
+ # Time / depth
74
+ "water_depth_to_time",
75
+ # Gain functions
76
+ "apply_tvg",
77
+ "tv_gamma",
78
+ "power_gain_1",
79
+ "power_gain_2",
80
+ "power_gain_3",
81
+ # Masking
82
+ "clear_water",
83
+ "clear_multiples",
84
+ # Filters
85
+ "mfv_fltr",
86
+ "scale_to_range",
87
+ ]