asp-plot 2.2.0__tar.gz → 3.0.0__tar.gz

{asp_plot-2.2.0 → asp_plot-3.0.0}/AGENTS.md

@@ -54,7 +54,7 @@ sphinx-autobuild docs docs/_build/html --open-browser   # or sphinx-build for a
 ## External Data Sources
 
 - **ICESat-2 ATL06-SR** (Earth): requested through the SlideRule API; results cached as parquet next to the report.
-- **LOLA (Moon) / MOLA (Mars)**: async queries to the ODE GDS REST API via the `request_planetary_altimetry` CLI — the user gets a download link by email, then passes the CSV to `asp_report --altimetry_csv`. Coordinates are east-positive 0–360 longitude, planetocentric latitude.
+- **LOLA (Moon) / MOLA (Mars)**: async queries to the ODE GDS REST API via the `request_planetary_altimetry` CLI — the user gets a download link by email, then passes the CSV to `asp_report --altimetry-csv`. Coordinates are east-positive 0–360 longitude, planetocentric latitude.
 
 ## Testing
 

{asp_plot-2.2.0 → asp_plot-3.0.0}/ARCHITECTURE.md

@@ -42,7 +42,7 @@ The package is organized by functionality, with each module focused on a specifi
 - `pixel_window_to_bbox()` / `bbox_to_pixel_offset()`: convert a detailed-hillshade clip between a DEM-CRS map bbox and a top-left pixel offset. `bbox_to_pixel_offset` uses `rowcol(..., op=round)` (round-to-nearest, **not** floor) so a replayed clip doesn't drift by a pixel from floating-point error
 - `reproject_bbox(bbox, src_crs, dst_crs)`: reprojects a clip bbox between CRSs (via `rasterio.warp.transform_bounds`) so clip reuse works across stereo variants in different projections (e.g. MOC non-mapproj Stereographic vs mapproj Sinusoidal). `plot_detailed_hillshade(clip_windows_crs=...)` passes the manifest's `dem_crs`; reprojection is a no-op when CRSs match
 - Deliberately imports nothing from `report.py` / `fpdf`, so it is safe to use from notebooks
-- The `asp_report` CLI always writes `<report_stem>_figure_selections.yml` next to the report; `--reuse_selections PATH` replays a prior run's choices
+- The `asp_report` CLI always writes `<report_stem>_figure_selections.yml` next to the report; `--reuse-selections PATH` replays a prior run's choices
 
 **`report.py`** - PDF report generation using fpdf2
 - `ReportSection`: Dataclass representing a report figure (title, image path, caption)
@@ -53,13 +53,13 @@ The package is organized by functionality, with each module focused on a specifi
 - `_add_processing_parameters_page()`: helper that renders the runtime summary table plus the bundle_adjust / stereo / point2dem / report commands on page 2 (moved from the trailing page as of v1.13.0). Also renders the reconstructed `mapproject` command(s) (from the optional `mapproject` list key; see `mapproject.py`) with a "reconstructed from output metadata" note.
 - `_fmt_sig()`: formats a number compactly — 2 decimals for |x| < 10, 1 decimal for 10 ≤ |x| < 100, 0 decimals above, "n/a" for non-finite. Used for alignment stats.
 - Title page displays: processing date, ASP version (from logs), asp_plot version (from package metadata)
-- Page order: title + DEM summary → Processing Parameters → diagnostic figures → (if `--pc_align` ran) alignment report page + aligned-DEM figures.
+- Page order: title + DEM summary → Processing Parameters → diagnostic figures → (if the `pc_align` step ran) alignment report page + aligned-DEM figures.
 - `report.py` is fed declaratively by `report_pipeline.py`; it was **not** rewritten in #128.
 
 **`report_pipeline.py`** - Declarative report pipeline behind the `asp_report` CLI (issue #128)
 - `ReportConfig`: dataclass packing the ~18 CLI options into one Click-free object (field names/defaults mirror the options one-for-one, guarded by a test)
 - `run_report(config)`: importable/callable from notebooks and tests with no Click context; returns the written PDF path
-- A declarative section registry (`REPORT_SECTIONS`) of `ReportSpec`s replaces the old inline plot-and-append wall: each spec pairs an `enabled(ctx)` predicate with a `build(ctx)` function returning the sections to append. `--plot_geometry` / `--plot_altimetry` / `--pc_align` gating are predicates; figure numbering comes from a per-run counter on the shared `ReportContext`, so section order and numbering are data, not source-line position. The alignment "Page B/C/D" follow-ups are one spec emitting several sections
+- A declarative section registry (`REPORT_SECTIONS`) of `ReportSpec`s replaces the old inline plot-and-append wall: each spec pairs an `enabled(ctx)` predicate with a `build(ctx)` function returning the sections to append. `--no-geometry` / `--no-altimetry` / `--no-pc-align` gating are predicates; figure numbering comes from a per-run counter on the shared `ReportContext`, so section order and numbering are data, not source-line position. The alignment "Page B/C/D" follow-ups are one spec emitting several sections
 - Section builders: `_build_input_scenes`, `_build_stereo_geometry`, `_build_match_points`, `_build_bundle_adjust`, `_build_disparity`, `_build_dem_results`, `_build_detailed_hillshade`, `_build_altimetry` (→ `_build_altimetry_earth` / `_build_altimetry_planetary`)
 - `_numbered_sections()`: shared helper turning a plotter's saved-filename list into one `ReportSection` per figure (first gets the caption, continuations are titled "... (continued)") — used by the scenes/geometry/match/disparity builders, whose plotters save one figure per pair on multi-view runs (issue #160)
 
@@ -218,28 +218,27 @@ All CLI tools are in `asp_plot/cli/` and use Click for argument parsing:
 **`asp_report.py`** - Main CLI tool (`asp_report` command)
 - Generates comprehensive PDF reports of ASP processing
 - A **thin Click wrapper** (issue #128): parses the ~18 options into a `ReportConfig` and calls `report_pipeline.run_report(config)`. All orchestration lives in `report_pipeline.py` (see the module structure section); the CLI file itself is now just option definitions + the `ReportConfig` build
-- Accepts directories for stereo and bundle_adjust outputs
+- Accepts a directory for stereo outputs and a directory or ASP-style prefix for bundle_adjust outputs; trailing slashes are tolerated (issue #60)
 - Options for reference DEMs, ICESat-2 comparisons, basemaps
 - Report section order: Input Scenes → Stereo Geometry → Match Points → Bundle Adjust panels (Log/Linear Residuals, Map-Projected Residuals, Geodiff) → Disparity → DEM Results → Detailed Hillshade → Altimetry panels. Disparity follows Bundle Adjust (not Hillshade) and DEM Results precedes Hillshade, so the title page → inputs → per-step diagnostics → final DEM products narrative reads top-down.
 - Title-page `ReportMetadata` is populated here; `get_acquisition_dates()` is called with the main directory plus stereo/BA subdirs as `extra_dirs` so the Acquisition Date(s) row appears on both raw-input layouts (WV XMLs at top level) and layouts where XMLs live one level deep.
 - `--directory`: Root ASP processing directory (default: `./`)
-- `--stereo_directory`: Stereo output subdirectory (default: `stereo`)
-- `--bundle_adjust_directory`: Optional BA directory
-- `--dem_filename`: Custom DEM filename (default: auto-detect `*-DEM.tif`)
-- `--dem_gsd`: Custom DEM ground sample distance
-- `--map_crs`: Projection as `EPSG:XXXX` (default: auto-detect from DEM, fallback `EPSG:4326`)
-- `--reference_dem`: Reference DEM path (auto-detected from logs if not supplied)
-- `--add_basemap`: Add Esri WorldImagery basemaps (default: True, requires internet)
-- `--plot_altimetry`: Plot altimetry comparisons (default: True). Auto-detects planetary body from DEM CRS: Earth → ICESat-2 (requires internet), Moon → LOLA, Mars → MOLA. For planetary DEMs, requires `--altimetry_csv`. Replaces the deprecated `--plot_icesat` flag.
-- `--plot_icesat`: Deprecated alias for `--plot_altimetry`. Prints deprecation warning if used.
-- `--altimetry_csv`: Path to a LOLA/MOLA CSV from the ODE GDS API. **Mars: must be the `*_pts_csv.csv` (not `*_topo_csv.csv`) — the loader requires the `PLANET_RAD` column to avoid the oblate-areoid offset.** Moon accepts either the `*_topo_simple_csv.csv` (results=u) or the `*_pts_csv.csv` (results=p). Obtained via the `request_planetary_altimetry` CLI tool.
-- `--pc_align`: If True (default) and `--plot_altimetry` is True, runs `pc_align` against the reference altimetry (ICESat-2 for Earth, MOLA for Mars, LOLA for Moon) after the existing altimetry plots and appends an alignment report. **Earth success path**: adds four pages (alignment report page, pre/post landcover histogram, aligned profile, aligned best/worst segments). **Planetary success path**: adds three pages (alignment report page, pre/post mapview, pre/post histogram). `insufficient_points` and `no_improvement` outcomes emit a single alignment report page on either branch. Disabled automatically when `--plot_altimetry` / `--plot_icesat` is False.
-- `--plot_geometry`: Plot stereo geometry (default: True; disable for planetary missions)
-- `--subset_km`: Hillshade subset size in km (default: 1.0)
-- `--atl06sr_time_range`: Time range for ICESat-2 ATL06-SR requests. `"all"` (default) for full mission, `"auto"` for scene metadata ±1 year, `"START,END"` for a custom range, or a single date (buffered by ±1 year).
-- `--reuse_selections`: Path to a `*_figure_selections.yml` from a prior run. Replays that run's ICESat-2 points (parquet), profile track, best/worst segments, and detailed-hillshade clips so re-processing runs (e.g. mapproj vs non-mapproj) are directly comparable (issue #121). Every run always writes `<report_stem>_figure_selections.yml` next to the report (the `regenerate_reports.sh` paired variants use this to reuse each other). Generated sidecars are gitignored (they hardcode absolute local paths); a sanitized example is in `docs/cli/asp_report.md`.
-- `--report_filename`: PDF report filename or path. A bare filename saves in the stereo directory; a path (e.g. `reports/report.pdf`) is used as-is. Default is auto-generated as `asp_report_<report_title>_<UTC timestamp>.pdf`
-- `--report_title`: Custom report title (default: directory name)
+- `--stereo-directory`: Stereo output subdirectory (default: `stereo`)
+- `--bundle-adjust-prefix`: Optional BA output location — either a directory (`ba`) or an ASP-style output prefix (`ba/run`, as passed to stereo/mapproject); a prefix narrows file globs to that run's outputs
+- `--dem-filename`: Custom DEM filename (default: auto-detect `*-DEM.tif`)
+- `--dem-gsd`: Custom DEM ground sample distance
+- `--map-crs`: Projection as `EPSG:XXXX` (default: auto-detect from DEM, fallback `EPSG:4326`)
+- `--reference-dem`: Reference DEM path (auto-detected from logs if not supplied)
+- `--no-basemap`: Skip the Esri WorldImagery basemaps added by default (which require internet)
+- `--no-altimetry`: Skip the altimetry comparisons plotted by default. Auto-detects planetary body from DEM CRS: Earth → ICESat-2 (requires internet), Moon → LOLA, Mars → MOLA. For planetary DEMs, requires `--altimetry-csv`.
+- `--altimetry-csv`: Path to a LOLA/MOLA CSV from the ODE GDS API. **Mars: must be the `*_pts_csv.csv` (not `*_topo_csv.csv`) — the loader requires the `PLANET_RAD` column to avoid the oblate-areoid offset.** Moon accepts either the `*_topo_simple_csv.csv` (results=u) or the `*_pts_csv.csv` (results=p). Obtained via the `request_planetary_altimetry` CLI tool.
+- `--no-pc-align`: Skips the `pc_align` step; by default (when altimetry is on) the report runs `pc_align` against the reference altimetry (ICESat-2 for Earth, MOLA for Mars, LOLA for Moon) after the existing altimetry plots and appends an alignment report. **Earth success path**: adds four pages (alignment report page, pre/post landcover histogram, aligned profile, aligned best/worst segments). **Planetary success path**: adds three pages (alignment report page, pre/post mapview, pre/post histogram). `insufficient_points` and `no_improvement` outcomes emit a single alignment report page on either branch. Skipped automatically when `--no-altimetry` is set.
+- `--no-geometry`: Skip the stereo geometry plots drawn by default (used for planetary missions)
+- `--subset-km`: Hillshade subset size in km (default: 1.0)
+- `--atl06sr-time-range`: Time range for ICESat-2 ATL06-SR requests. `"all"` (default) for full mission, `"auto"` for scene metadata ±1 year, `"START,END"` for a custom range, or a single date (buffered by ±1 year).
+- `--reuse-selections`: Path to a `*_figure_selections.yml` from a prior run. Replays that run's ICESat-2 points (parquet), profile track, best/worst segments, and detailed-hillshade clips so re-processing runs (e.g. mapproj vs non-mapproj) are directly comparable (issue #121). Every run always writes `<report_stem>_figure_selections.yml` next to the report (the `regenerate_reports.sh` paired variants use this to reuse each other). Generated sidecars are gitignored (they hardcode absolute local paths); a sanitized example is in `docs/cli/asp_report.md`.
+- `--report-filename`: PDF report filename or path. A bare filename saves in the stereo directory; a path (e.g. `reports/report.pdf`) is used as-is. Default is auto-generated as `asp_report_<report_title>_<UTC timestamp>.pdf`
+- `--report-title`: Custom report title (default: directory name)
 
 **`csm_camera_plot.py`** - CSM camera comparison tool (`csm_camera_plot` command)
 - Wrapper for `csm_camera.py` functions
@@ -253,7 +252,7 @@ All CLI tools are in `asp_plot/cli/` and use Click for argument parsing:
 - `--email`: Email for notification when query finishes (required)
 - `--channels`: LOLA detector channels (Moon only, default `tffff` = channel 1 only)
 - Saves request metadata as `altimetry_request_info.yml` alongside the DEM
-- Workflow: submit query → receive email → download/unzip → pass `*_pts_csv.csv` (Mars) or `*_topo_simple_csv.csv`/`*_pts_csv.csv` (Moon) to `asp_report --altimetry_csv`
+- Workflow: submit query → receive email → download/unzip → pass `*_pts_csv.csv` (Mars) or `*_topo_simple_csv.csv`/`*_pts_csv.csv` (Moon) to `asp_report --altimetry-csv`
 
 **`stereo_geom.py`** - Stereo geometry visualization tool (`stereo_geom` command)
 - Wrapper for `StereoGeometryPlotter`
@@ -265,7 +264,7 @@ All CLI tools are in `asp_plot/cli/` and use Click for argument parsing:
 **`gallery.py`** - DEM gallery tool (`gallery` command)
 - Wrapper for `GalleryPlotter`; lays out many DEMs as a grid sharing one color scale
 - `--directory` + `--pattern` (supports recursive `**` for subdirectories) or an explicit list of `FILES` (files take precedence)
-- `--hillshade/--no-hillshade`, `--cmap`, `--downsample`, `--max_filesize_mb`, `--title`, `--output_directory/--output_filename`
+- `--no-hillshade`, `--cmap`, `--downsample`, `--max-filesize-mb`, `--title`, `--output-directory/--output-filename`
 - Saves `<dirname>_gallery.png` into the input directory by default
 
 ## Documentation Website
@@ -307,7 +306,7 @@ docs/
 - **`html_extra_path`** is used to serve `notebooks/figures/` at the correct relative path for notebook `<img src>` references.
 - **`docs/` is excluded from sdist** in `pyproject.toml` so docs never ship in the PyPI/conda package.
 - **Changelog** uses `{include} ../CHANGELOG.md` so there's one source of truth.
-- **Selective notebook exclusion**: `.readthedocs.yaml`'s `pre_build` copies every `notebooks/**/*.ipynb` into `docs/examples/notebooks/`, but specific notebooks can be dropped from the build by listing them in `exclude_patterns` in `docs/conf.py` (e.g., `worldview_utqiagvik_stereo.ipynb`). Inter-notebook links in the WorldView examples use fully-qualified `https://asp-plot.readthedocs.io/en/latest/...` URLs so they resolve both on RTD and in raw notebook previews. Report-link convention: each notebook's "Full Report Generation" section ends with a `#### See the resulting [report](https://asp-plot.readthedocs.io/en/latest/_static/reports/<filename>.pdf).` line that links directly to the PDF served from `_static/reports/`. The `<filename>` must match what the cell's `!asp_report --report_filename` writes (so the URL on RTD actually resolves).
+- **Selective notebook exclusion**: `.readthedocs.yaml`'s `pre_build` copies every `notebooks/**/*.ipynb` into `docs/examples/notebooks/`, but specific notebooks can be dropped from the build by listing them in `exclude_patterns` in `docs/conf.py` (e.g., `worldview_utqiagvik_stereo.ipynb`). Inter-notebook links in the WorldView examples use fully-qualified `https://asp-plot.readthedocs.io/en/latest/...` URLs so they resolve both on RTD and in raw notebook previews. Report-link convention: each notebook's "Full Report Generation" section ends with a `#### See the resulting [report](https://asp-plot.readthedocs.io/en/latest/_static/reports/<filename>.pdf).` line that links directly to the PDF served from `_static/reports/`. The `<filename>` must match what the cell's `!asp_report --report-filename` writes (so the URL on RTD actually resolves).
 
 ### Dependencies
 
@@ -337,7 +336,7 @@ Docs dependencies are in `pyproject.toml` under `[project.optional-dependencies]
 
 **ODE GDS REST API**: Base URL `https://oderest.rsl.wustl.edu/livegds`. Queries are submitted via `gds_query_async()` in async mode. The `request_planetary_altimetry` CLI submits the query and the user downloads results via email link. Coordinates use east-positive 0-360 longitude and planetocentric latitude.
 
-**Basemaps**: Uses `contextily` to fetch Esri WorldImagery tiles (requires internet). Can be disabled with `--add_basemap False`. Automatically skipped for planetary (non-Earth) DEMs.
+**Basemaps**: Uses `contextily` to fetch Esri WorldImagery tiles (requires internet). Can be disabled with `--no-basemap`. Automatically skipped for planetary (non-Earth) DEMs.
 
 ## Example Notebooks
 

{asp_plot-2.2.0 → asp_plot-3.0.0}/CHANGELOG.md

@@ -5,6 +5,22 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.0.0] - 2026-08-24
+
+A breaking standardization of the command-line interfaces ([#60](https://github.com/uw-cryo/asp_plot/issues/60)), done deliberately as a clean break — no aliases, no deprecation period — while the user base is small. Every multi-word option across the five CLIs (`asp_report`, `stereo_geom`, `csm_camera_plot`, `gallery`, `request_planetary_altimetry`) moves from underscores to the hyphenated style ASP itself uses (`--stereo_directory` → `--stereo-directory`), booleans become single switches for the non-default behavior (`--add_basemap False` → `--no-basemap`), and `--bundle_adjust_directory` becomes `--bundle-adjust-prefix`, matching both the name and the semantics of ASP's own option. The Python API is unchanged.
+
+A major version because every existing `asp_report`/`stereo_geom`/`csm_camera_plot`/`gallery` invocation with a multi-word or boolean option needs editing. **Upgrade:** re-spell the flags per the entries below — the `--help` of each command lists the new names, and the committed example reports and notebooks show them in use. No new dependencies and no entry-point changes.
+
+### Changed
+- **All CLI options are hyphenated** (issue [#60](https://github.com/uw-cryo/asp_plot/issues/60)). One-for-one renames: `--stereo-directory`, `--dem-filename`, `--dem-gsd`, `--map-crs`, `--reference-dem`, `--altimetry-csv`, `--subset-km`, `--atl06sr-time-range`, `--reuse-selections`, `--report-filename`, `--report-title` (asp_report); `--output-directory`, `--output-filename` (stereo_geom, gallery); `--max-filesize-mb` (gallery); `--original-cameras`, `--optimized-cameras`, `--map-crs`, `--upper-magnitude-percentile` (csm_camera_plot). Single-word options are untouched. The command recorded on the report's final page is emitted with the new spellings, so it stays re-runnable.
+- **Boolean options are now single switches for the non-default behavior**, in the Unix idiom: where the default is on, only the negative switch exists — `--no-basemap`, `--no-altimetry`, `--no-pc-align`, `--no-geometry` (asp_report), `--no-basemap` (stereo_geom), `--no-trim` (csm_camera_plot), `--no-hillshade` (gallery, replacing the `--hillshade/--no-hillshade` pair) — and where the default is off, only the positive one — `--shared-scales`, `--log-scale-positions`, `--log-scale-angles`, `--add-basemap` (csm_camera_plot). Where you passed `--add_basemap False`, pass `--no-basemap`; the verb-y `plot`/`add` prefixes are dropped from the switch names.
+- **`--bundle_adjust_directory` is now `--bundle-adjust-prefix`**, and accepts either the containing directory (`ba`, the previous behavior) or the same ASP-style output prefix passed to `stereo`/`mapproject` (`ba/run`). A prefix narrows the residuals/log file search to that run's outputs, so several bundle-adjust runs can share a directory. Internally, `ReportConfig.bundle_adjust_directory` is renamed to `bundle_adjust_prefix`.
+- **`csm_camera_plot` options are harmonized with the other CLIs and ASP's `orbit_plot.py`**: `--save_dir` → `--output-directory`, `--fig_fn` → `--output-filename`, `--figsize` → `--figure-size`. The `csm_camera_summary_plot()` Python keyword arguments are unchanged.
+- **Trailing slashes on directory options are stripped centrally** (`--directory`, `--stereo-directory`, `--bundle-adjust-prefix`), closing the last thread of issue [#60](https://github.com/uw-cryo/asp_plot/issues/60); the dg_mosaic `r100` concern from the same issue was resolved earlier by the sensor readers, which treat `*.r100.xml`/`*.r50.xml` as regenerable intermediates.
+
+### Removed
+- **The deprecated `--plot_icesat` alias** (deprecated in favor of `--plot_altimetry` in 1.10.0) is gone; altimetry is on by default and `--no-altimetry` disables it.
+
 ## [2.2.0] - 2026-08-18
 
 A correctness release for the CSM camera comparison, and a new diagnostic layer under the match points.

{asp_plot-2.2.0 → asp_plot-3.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: asp_plot
-Version: 2.2.0
+Version: 3.0.0
 Summary: Package for plotting outputs Ames Stereo Pipeline processing
 Project-URL: Homepage, https://github.com/uw-cryo/asp_plot
 Project-URL: Documentation, https://asp-plot.readthedocs.io
@@ -74,7 +74,7 @@ See the [installation guide](https://asp-plot.readthedocs.io/en/latest/installat
 Generate a PDF report from an ASP processing directory:
 
 ```
-asp_report --directory ./ --stereo_directory stereo
+asp_report --directory ./ --stereo-directory stereo
 ```
 
 See the [CLI documentation](https://asp-plot.readthedocs.io/en/latest/cli/index.html) for all options and additional tools (`stereo_geom`, `csm_camera_plot`).

{asp_plot-2.2.0 → asp_plot-3.0.0}/README.md

@@ -30,7 +30,7 @@ See the [installation guide](https://asp-plot.readthedocs.io/en/latest/installat
 Generate a PDF report from an ASP processing directory:
 
 ```
-asp_report --directory ./ --stereo_directory stereo
+asp_report --directory ./ --stereo-directory stereo
 ```
 
 See the [CLI documentation](https://asp-plot.readthedocs.io/en/latest/cli/index.html) for all options and additional tools (`stereo_geom`, `csm_camera_plot`).

{asp_plot-2.2.0 → asp_plot-3.0.0}/asp_plot/bundle_adjust.py

@@ -41,7 +41,7 @@ class ReadBundleAdjustFiles:
     >>> mapproj_gdf = ba_reader.get_mapproj_residuals_gdf()
     """
 
-    def __init__(self, directory, bundle_adjust_directory):
+    def __init__(self, directory, bundle_adjust_directory, stem=None):
         """
         Initialize the ReadBundleAdjustFiles object.
 
@@ -51,10 +51,15 @@ class ReadBundleAdjustFiles:
             Root directory of ASP processing
         bundle_adjust_directory : str
             Subdirectory containing bundle adjustment outputs
+        stem : str, optional
+            Run stem of an ASP output prefix (the ``run`` in ``ba/run``).
+            When given, file globs are narrowed to that run's outputs;
+            otherwise any run in the directory matches.
         """
         self.directory = os.path.expanduser(directory)
         self.bundle_adjust_directory = bundle_adjust_directory
         self.full_directory = os.path.join(self.directory, bundle_adjust_directory)
+        self.stem_glob = stem if stem else "*"
 
     def get_csv_paths(self, geodiff_files=False):
         """
@@ -86,8 +91,8 @@ class ReadBundleAdjustFiles:
         will attempt to generate them using the geodiff ASP tool.
         """
         filenames = [
-            "*-initial_residuals_pointmap.csv",
-            "*-final_residuals_pointmap.csv",
+            f"{self.stem_glob}-initial_residuals_pointmap.csv",
+            f"{self.stem_glob}-final_residuals_pointmap.csv",
         ]
 
         if geodiff_files:
@@ -371,7 +376,9 @@ class ReadBundleAdjustFiles:
         the distance between matched interest points in the map-projected
         images after bundle adjustment.
         """
-        path = glob_file(self.full_directory, "*-mapproj_match_offsets.txt")
+        path = glob_file(
+            self.full_directory, f"{self.stem_glob}-mapproj_match_offsets.txt"
+        )
         if path is None:
             raise ValueError("\n\nMapProj Residuals TXT file not found.\n\n")
 
@@ -411,7 +418,9 @@ class ReadBundleAdjustFiles:
         the bundle adjustment residuals propagate to uncertainty in
         triangulation. This is an estimate of the final DEM error.
         """
-        path = glob_file(self.full_directory, "*-triangulation_uncertainty.txt")
+        path = glob_file(
+            self.full_directory, f"{self.stem_glob}-triangulation_uncertainty.txt"
+        )
         if path is None:
             raise ValueError("\n\nTriangulation Uncertainty TXT file not found.\n\n")
 

{asp_plot-2.2.0 → asp_plot-3.0.0}/asp_plot/cli/asp_report.py

@@ -16,7 +16,10 @@ def _reconstruct_command():
     for param in click_ctx.command.params:
         val = click_ctx.params.get(param.name)
         if val is not None and val != param.default:
-            cmd_parts.append(f"--{param.name} {shlex.quote(str(val))}")
+            if param.is_bool_flag:
+                cmd_parts.append(param.opts[0])
+            else:
+                cmd_parts.append(f"{param.opts[0]} {shlex.quote(str(val))}")
     return " ".join(cmd_parts)
 
 
@@ -28,123 +31,116 @@ def _reconstruct_command():
     help="Required directory of ASP processing with scenes and sub-directories for stereo and optionally bundle adjustment. Default: current directory.",
 )
 @click.option(
-    "--bundle_adjust_directory",
+    "--bundle-adjust-prefix",
     prompt=False,
     default=None,
-    help="Optional directory of bundle adjustment files. If expected *residuals_pointmap.csv files are not found in the supplied directory, no bundle adjustment plots will be generated. Default: None.",
+    help="Optional bundle adjustment output location, relative to --directory. Accepts either a directory (e.g. 'ba') or an ASP-style output prefix as passed to --bundle-adjust-prefix in stereo/mapproject (e.g. 'ba/run'). If expected *residuals_pointmap.csv files are not found there, no bundle adjustment plots will be generated. Default: None.",
 )
 @click.option(
-    "--stereo_directory",
+    "--stereo-directory",
     prompt=True,
     default="stereo",
     help="Required directory of stereo files. Default: stereo.",
 )
 @click.option(
-    "--dem_filename",
+    "--dem-filename",
     prompt=False,
     default=None,
     help="Optional DEM filename in the stereo directory. Default: None, which will search for the *-DEM.tif file in the stereo directory. Specify it as the basename with extension, e.g. my-custom-dem-name.tif.",
 )
 @click.option(
-    "--dem_gsd",
+    "--dem-gsd",
     prompt=False,
     default=None,
     help="Optional ground sample distance of the DEM. Default: None, which will search for the *-DEM.tif file in the stereo directory. If there is a GSD in the name of the file, specify it here as a float or integer, e.g. 1, 1.5, etc.",
 )
 @click.option(
-    "--map_crs",
+    "--map-crs",
     prompt=False,
     default=None,
     help="Projection for altimetry and bundle adjustment plots. As EPSG:XXXX. Default: None, which will use the projection of the ASP DEM, and fall back on EPSG:4326 if not found.",
 )
 @click.option(
-    "--reference_dem",
+    "--reference-dem",
     prompt=False,
     default=None,
     help="Optional reference DEM used in ASP processing. No default. If not supplied, the logs will be examined to find it. If not found, no difference plots will be generated.",
 )
 @click.option(
-    "--add_basemap",
-    prompt=False,
-    default=True,
-    help="If True, add a basemaps to the figures, which requires internet connection. Default: True.",
-)
-@click.option(
-    "--plot_altimetry",
-    prompt=False,
-    default=True,
-    help="If True, plot altimetry comparisons (ICESat-2 for Earth, LOLA for Moon, MOLA for Mars). For planetary DEMs, requires --altimetry_csv. Default: True.",
+    "--no-basemap",
+    is_flag=True,
+    default=False,
+    help="Skip the figure basemaps (basemaps are added by default, which requires an internet connection).",
 )
 @click.option(
-    "--plot_icesat",
-    prompt=False,
-    default=None,
-    help="Deprecated: use --plot_altimetry instead. Kept for backward compatibility.",
+    "--no-altimetry",
+    is_flag=True,
+    default=False,
+    help="Skip the altimetry comparisons (plotted by default: ICESat-2 for Earth, LOLA for Moon, MOLA for Mars; planetary DEMs require --altimetry-csv).",
 )
 @click.option(
-    "--altimetry_csv",
+    "--altimetry-csv",
     prompt=False,
     default=None,
     type=click.Path(exists=True),
     help="Path to a LOLA/MOLA *_topo_csv.csv file from the ODE GDS API. Required for planetary altimetry plots. Obtain via: request_planetary_altimetry --dem <dem> --email <email>, then download and unzip the result.",
 )
 @click.option(
-    "--pc_align",
-    prompt=False,
-    default=True,
-    help="If True and --plot_altimetry is True, run pc_align against the reference altimetry (ICESat-2 for Earth, MOLA for Mars, LOLA for Moon) and append the alignment-report pages. Disabled automatically when --plot_altimetry / --plot_icesat is False. Default: True.",
+    "--no-pc-align",
+    is_flag=True,
+    default=False,
+    help="Skip the pc_align step (run by default against the reference altimetry -- ICESat-2 for Earth, MOLA for Mars, LOLA for Moon -- appending the alignment-report pages; skipped automatically with --no-altimetry).",
 )
 @click.option(
-    "--plot_geometry",
-    prompt=False,
-    default=True,
-    help="If True, plot the stereo geometry. Default: True.",
+    "--no-geometry",
+    is_flag=True,
+    default=False,
+    help="Skip the stereo geometry plots (plotted by default).",
 )
 @click.option(
-    "--subset_km",
+    "--subset-km",
     prompt=False,
     default=1.0,
     help="Size in km of the subset to plot for the detailed hillshade. Default: 1 km.",
 )
 @click.option(
-    "--atl06sr_time_range",
+    "--atl06sr-time-range",
     prompt=False,
     default="all",
     help='Time range for ICESat-2 ATL06-SR data requests. "all" for all available data (mission start to present), or "START,END" for a custom range (e.g. "2020-01-01,2024-12-31"), or "auto" for scene metadata +/- 1 year. Default: all.',
 )
 @click.option(
-    "--reuse_selections",
+    "--reuse-selections",
     prompt=False,
     default=None,
     type=click.Path(exists=True),
     help="Path to a *_figure_selections.yml written by a previous run. When supplied, replays that run's ICESat-2 points (parquet), profile track, best/worst segments, and detailed-hillshade clip boxes so figures are directly comparable across re-processing runs. Default: None.",
 )
 @click.option(
-    "--report_filename",
+    "--report-filename",
     prompt=False,
     default=None,
     help="PDF report filename or path. A bare filename (e.g. 'report.pdf') is saved in the stereo directory. A path (e.g. 'reports/report.pdf' or '/tmp/report.pdf') is used as-is. Default: auto-generated from directory name.",
 )
 @click.option(
-    "--report_title",
+    "--report-title",
     prompt=False,
     default=None,
     help="Title for the report. Default: Directory name of ASP processing.",
 )
 def main(
     directory,
-    bundle_adjust_directory,
+    bundle_adjust_prefix,
     stereo_directory,
     dem_filename,
     dem_gsd,
     map_crs,
     reference_dem,
-    add_basemap,
-    plot_altimetry,
-    plot_icesat,
+    no_basemap,
+    no_altimetry,
     altimetry_csv,
-    pc_align,
-    plot_geometry,
+    no_pc_align,
+    no_geometry,
     subset_km,
     atl06sr_time_range,
     reuse_selections,
@@ -160,18 +156,17 @@ def main(
     """
     config = ReportConfig(
         directory=directory,
-        bundle_adjust_directory=bundle_adjust_directory,
+        bundle_adjust_prefix=bundle_adjust_prefix,
         stereo_directory=stereo_directory,
         dem_filename=dem_filename,
         dem_gsd=dem_gsd,
         map_crs=map_crs,
         reference_dem=reference_dem,
-        add_basemap=add_basemap,
-        plot_altimetry=plot_altimetry,
-        plot_icesat=plot_icesat,
+        add_basemap=not no_basemap,
+        plot_altimetry=not no_altimetry,
         altimetry_csv=altimetry_csv,
-        pc_align=pc_align,
-        plot_geometry=plot_geometry,
+        pc_align=not no_pc_align,
+        plot_geometry=not no_geometry,
         subset_km=subset_km,
         atl06sr_time_range=atl06sr_time_range,
         reuse_selections=reuse_selections,

{asp_plot-2.2.0 → asp_plot-3.0.0}/asp_plot/cli/csm_camera_plot.py

@@ -6,19 +6,19 @@ from asp_plot.csm_camera import csm_camera_summary_plot
 
 @click.command()
 @click.option(
-    "--original_cameras",
+    "--original-cameras",
     prompt=True,
     default="",
     help="Original camera files, supplied as comma separated list 'path/to/original_camera_1,path/to/original_camera_2'. No default. Must be supplied.",
 )
 @click.option(
-    "--optimized_cameras",
+    "--optimized-cameras",
     prompt=True,
     default="",
     help="Optimized camera files, supplied as comma separated list 'path/to/optimized_camera_1,path/to/optimized_camera_2'. No default. Must be supplied.",
 )
 @click.option(
-    "--map_crs",
+    "--map-crs",
     prompt=False,
     default=None,
     help="UTM EPSG code for map projection. As EPSG:XXXX. If not supplied, the map will be plotted in original camera coordinates of EPSG:4978 (ECEF).",
@@ -30,73 +30,73 @@ from asp_plot.csm_camera import csm_camera_summary_plot
     help="Optional short title to append to figure output. Default: None.",
 )
 @click.option(
-    "--trim",
-    prompt=False,
-    default=True,
-    help="Trim the beginning and end of the positions plotted to the first and last camera image lines. Default: True.",
+    "--no-trim",
+    is_flag=True,
+    default=False,
+    help="Do not trim the plotted positions to the first and last camera image lines (trimmed by default).",
 )
 @click.option(
-    "--shared_scales",
-    prompt=False,
+    "--shared-scales",
+    is_flag=True,
     default=False,
-    help="If True, the position and angle difference scales are shared between each camera. Default: False.",
+    help="Share the position and angle difference scales between the cameras.",
 )
 @click.option(
-    "--log_scale_positions",
-    prompt=False,
+    "--log-scale-positions",
+    is_flag=True,
     default=False,
-    help="If True, the position difference scales are log scaled. Default: False.",
+    help="Log-scale the position difference plots.",
 )
 @click.option(
-    "--log_scale_angles",
-    prompt=False,
+    "--log-scale-angles",
+    is_flag=True,
     default=False,
-    help="If True, the angle difference scales are log scaled. Default: False.",
+    help="Log-scale the angle difference plots.",
 )
 @click.option(
-    "--upper_magnitude_percentile",
+    "--upper-magnitude-percentile",
     prompt=False,
     default=95,
     help="Percentile to use for the upper limit of the mapview colorbars. Default: 95.",
 )
 @click.option(
-    "--figsize",
+    "--figure-size",
     prompt=False,
     default="20,15",
     help="Figure size as width,height. Default: 20,15.",
     callback=lambda ctx, param, value: tuple(map(int, value.split(","))),
 )
 @click.option(
-    "--save_dir",
+    "--output-directory",
     prompt=False,
     default=None,
     help="Directory to save the figure. Default: None, which does not save the figure.",
 )
 @click.option(
-    "--fig_fn",
+    "--output-filename",
     prompt=False,
     default="csm_camera_summary_plot.png",
     help="Figure filename. Default: csm_camera_summary_plot.png.",
 )
 @click.option(
-    "--add_basemap",
-    prompt=False,
+    "--add-basemap",
+    is_flag=True,
     default=False,
-    help="If True, add a contextily basemap to the figure, which requires internet connection. Default: False.",
+    help="Add a contextily basemap to the figure, which requires an internet connection.",
 )
 def main(
     original_cameras,
     optimized_cameras,
     map_crs,
     title,
-    trim,
+    no_trim,
     shared_scales,
     log_scale_positions,
     log_scale_angles,
     upper_magnitude_percentile,
-    figsize,
-    save_dir,
-    fig_fn,
+    figure_size,
+    output_directory,
+    output_filename,
     add_basemap,
 ):
     """
@@ -127,14 +127,14 @@ def main(
         cam2_list,
         map_crs.split(":")[-1] if map_crs else None,
         title=title,
-        trim=trim,
+        trim=not no_trim,
         shared_scales=shared_scales,
         log_scale_positions=log_scale_positions,
         log_scale_angles=log_scale_angles,
         upper_magnitude_percentile=upper_magnitude_percentile,
-        figsize=figsize,
-        save_dir=save_dir,
-        fig_fn=fig_fn,
+        figsize=figure_size,
+        save_dir=output_directory,
+        fig_fn=output_filename,
         add_basemap=add_basemap,
         **ctx_kwargs,
     )

{asp_plot-2.2.0 → asp_plot-3.0.0}/asp_plot/cli/gallery.py

@@ -20,9 +20,10 @@ from asp_plot.gallery import GalleryPlotter
 )
 @click.argument("files", nargs=-1, type=click.Path(exists=True))
 @click.option(
-    "--hillshade/--no-hillshade",
-    default=True,
-    help="Draw a gray hillshade underlay beneath each DEM. Default: True.",
+    "--no-hillshade",
+    is_flag=True,
+    default=False,
+    help="Skip the gray hillshade underlay drawn beneath each DEM by default.",
 )
 @click.option(
     "--cmap",
@@ -37,7 +38,7 @@ from asp_plot.gallery import GalleryPlotter
     help="Downsample factor for reads, or 'auto' to size thumbnails automatically. Default: auto.",
 )
 @click.option(
-    "--max_filesize_mb",
+    "--max-filesize-mb",
     prompt=False,
     default=10.0,
     type=float,
@@ -50,13 +51,13 @@ from asp_plot.gallery import GalleryPlotter
     help="Figure suptitle. Default: none.",
 )
 @click.option(
-    "--output_directory",
+    "--output-directory",
     prompt=False,
     default=None,
     help="Directory to save the output plot. Default: Input directory.",
 )
 @click.option(
-    "--output_filename",
+    "--output-filename",
     prompt=False,
     default=None,
     help="Filename for the output plot. Default: Directory name with _gallery.png suffix.",
@@ -65,7 +66,7 @@ def main(
     directory,
     pattern,
     files,
-    hillshade,
+    no_hillshade,
     cmap,
     downsample,
     max_filesize_mb,
@@ -110,7 +111,7 @@ def main(
     os.makedirs(output_directory, exist_ok=True)
 
     plotter.plot_gallery(
-        hillshade=hillshade,
+        hillshade=not no_hillshade,
         cmap=cmap,
         max_filesize_mb=max_filesize_mb,
         save_dir=output_directory,

{asp_plot-2.2.0 → asp_plot-3.0.0}/asp_plot/cli/request_planetary_altimetry.py

@@ -36,13 +36,13 @@ def main(dem, email, channels):
       1. Run this command with your DEM and email
       2. Wait for the email notification (may take minutes to hours)
       3. Download and unzip the result
-      4. Pass the *_topo_csv.csv to asp_plot via --altimetry_csv
+      4. Pass the *_topo_csv.csv to asp_plot via --altimetry-csv
 
     \b
     Example:
       request_planetary_altimetry --dem stereo/output-DEM.tif --email user@example.com
       # ... wait for email, download and unzip ...
-      asp_report --directory ./ --altimetry_csv /path/to/*_topo_csv.csv
+      asp_report --directory ./ --altimetry-csv /path/to/*_topo_csv.csv
     """
     from asp_plot.altimetry import GDS_BASE_URL, gds_query_async
 
@@ -53,7 +53,7 @@ def main(dem, email, channels):
         click.echo(
             "\nThis DEM is an Earth DEM. ICESat-2 altimetry is fetched "
             "automatically by asp_plot — no separate request needed.\n"
-            "Run: asp_report --directory <dir> --plot_altimetry True\n"
+            "Run: asp_report --directory <dir> (altimetry plots are on by default)\n"
         )
         sys.exit(0)
 
@@ -124,7 +124,7 @@ def main(dem, email, channels):
     click.echo(
         "\nYou will receive an email when the data is ready. "
         "Download and unzip the result, then pass the *_topo_csv.csv to asp_plot:\n"
-        "  asp_report --directory <dir> --altimetry_csv <*_topo_csv.csv>\n"
+        "  asp_report --directory <dir> --altimetry-csv <*_topo_csv.csv>\n"
     )
 
 

{asp_plot-2.2.0 → asp_plot-3.0.0}/asp_plot/cli/stereo_geom.py

@@ -17,19 +17,19 @@ from asp_plot.stereo_geometry import StereoGeometryPlotter
     ),
 )
 @click.option(
-    "--add_basemap",
-    prompt=False,
-    default=True,
-    help="If True, add a basemap to the figures, which requires internet connection. Default: True.",
+    "--no-basemap",
+    is_flag=True,
+    default=False,
+    help="Skip the figure basemaps (basemaps are added by default, which requires an internet connection).",
 )
 @click.option(
-    "--output_directory",
+    "--output-directory",
     prompt=False,
     default=None,
     help="Directory to save the output plot. Default: Input directory.",
 )
 @click.option(
-    "--output_filename",
+    "--output-filename",
     prompt=False,
     default=None,
     help=(
@@ -41,7 +41,7 @@ from asp_plot.stereo_geometry import StereoGeometryPlotter
 def main(
     inputs,
     directory,
-    add_basemap,
+    no_basemap,
     output_directory,
     output_filename,
 ):
@@ -72,14 +72,14 @@ def main(
     # Positional INPUTS take precedence; otherwise fall back to --directory.
     if inputs:
         inputs = [os.path.expanduser(i) for i in inputs]
-        plotter = StereoGeometryPlotter(inputs=inputs, add_basemap=add_basemap)
+        plotter = StereoGeometryPlotter(inputs=inputs, add_basemap=not no_basemap)
         source_desc = " ".join(inputs)
         # Base directory for default output paths (resolved by the parser).
         base_directory = plotter.directory
     else:
         base_directory = os.path.expanduser(directory or "./")
         plotter = StereoGeometryPlotter(
-            directory=base_directory, add_basemap=add_basemap
+            directory=base_directory, add_basemap=not no_basemap
         )
         source_desc = base_directory
 

{asp_plot-2.2.0 → asp_plot-3.0.0}/asp_plot/processing_parameters.py

@@ -54,7 +54,11 @@ class ProcessingParameters:
     """
 
     def __init__(
-        self, processing_directory, bundle_adjust_directory=None, stereo_directory=None
+        self,
+        processing_directory,
+        bundle_adjust_directory=None,
+        stereo_directory=None,
+        bundle_adjust_stem=None,
     ):
         """
         Initialize the ProcessingParameters object.
@@ -67,6 +71,10 @@ class ProcessingParameters:
             Subdirectory containing bundle adjustment outputs, default is None
         stereo_directory : str, optional
             Subdirectory containing stereo outputs, default is None
+        bundle_adjust_stem : str, optional
+            Run stem of an ASP output prefix (the ``run`` in ``ba/run``).
+            When given, the bundle adjustment log glob is narrowed to that
+            run; otherwise any run in the directory matches.
 
         Notes
         -----
@@ -92,8 +100,13 @@ class ProcessingParameters:
         # Locate log files. A missing directory (None) means that stage was not
         # requested -- not an error -- so we guard on it rather than catching a
         # blanket exception that would also hide real I/O problems.
+        ba_log_pattern = (
+            f"{bundle_adjust_stem}-log-bundle_adjust*.txt"
+            if bundle_adjust_stem
+            else "*log-bundle_adjust*.txt"
+        )
         self.bundle_adjust_log = (
-            glob_file(self.full_ba_directory, "*log-bundle_adjust*.txt")
+            glob_file(self.full_ba_directory, ba_log_pattern)
             if self.full_ba_directory
             else None
         )

{asp_plot-2.2.0 → asp_plot-3.0.0}/asp_plot/report_pipeline.py

@@ -41,7 +41,12 @@ from asp_plot.selections import (
 )
 from asp_plot.stereo import StereoPlotter
 from asp_plot.stereo_geometry import StereoGeometryPlotter, camera_files_from_stereo_run
-from asp_plot.utils import Raster, detect_planetary_body, get_acquisition_dates
+from asp_plot.utils import (
+    Raster,
+    detect_planetary_body,
+    get_acquisition_dates,
+    resolve_directory_or_prefix,
+)
 
 
 @dataclass
@@ -53,7 +58,7 @@ class ReportConfig:
     """
 
     directory: str = "./"
-    bundle_adjust_directory: Optional[str] = None
+    bundle_adjust_prefix: Optional[str] = None
     stereo_directory: str = "stereo"
     dem_filename: Optional[str] = None
     dem_gsd: Optional[float] = None
@@ -61,7 +66,6 @@ class ReportConfig:
     reference_dem: Optional[str] = None
     add_basemap: bool = True
     plot_altimetry: bool = True
-    plot_icesat: Optional[object] = None
     altimetry_csv: Optional[str] = None
     pc_align: bool = True
     plot_geometry: bool = True
@@ -74,6 +78,15 @@ class ReportConfig:
     # CLI builds this from the Click context; non-CLI callers may leave it None.
     report_command: Optional[str] = None
 
+    def __post_init__(self):
+        # Tolerate trailing slashes on directory-like inputs (issue #60) so
+        # path joins and basename-derived titles behave the same either way.
+        for attr in ("directory", "stereo_directory", "bundle_adjust_prefix"):
+            value = getattr(self, attr)
+            if value:
+                stripped = value.rstrip("/\\")
+                setattr(self, attr, stripped or value)
+
 
 @dataclass
 class ReportContext:
@@ -93,6 +106,9 @@ class ReportContext:
     stereo_plotter: StereoPlotter
     asp_dem: Optional[str]
     plot_altimetry: bool
+    # --bundle-adjust-prefix resolved into a subdirectory and optional run stem
+    ba_directory: Optional[str] = None
+    ba_stem: Optional[str] = None
     report_metadata: Optional[ReportMetadata] = None
     reuse_clip_windows: Optional[list] = None
     reuse_clip_windows_crs: Optional[str] = None
@@ -204,7 +220,9 @@ def _build_bundle_adjust(ctx: ReportContext) -> List[object]:
     cfg = ctx.config
     sections: List[object] = []
     try:
-        ba_files = ReadBundleAdjustFiles(cfg.directory, cfg.bundle_adjust_directory)
+        ba_files = ReadBundleAdjustFiles(
+            cfg.directory, ctx.ba_directory, stem=ctx.ba_stem
+        )
         resid_initial_gdf, resid_final_gdf = ba_files.get_initial_final_residuals_gdfs()
 
         plotter = PlotBundleAdjustFiles(
@@ -316,7 +334,7 @@ def _build_bundle_adjust(ctx: ReportContext) -> List[object]:
 
     except ValueError:
         print(
-            f"\n\nNo bundle adjustment files found in directory {os.path.join(cfg.directory, cfg.bundle_adjust_directory):}. If you want bundle adjustment plots, make sure you run the tool and supply the correct directory to asp_report.\n\n"
+            f"\n\nNo bundle adjustment files found in directory {os.path.join(cfg.directory, ctx.ba_directory):}. If you want bundle adjustment plots, make sure you run the tool and supply the correct --bundle-adjust-prefix to asp_report.\n\n"
         )
     return sections
 
@@ -400,7 +418,7 @@ def _build_altimetry_earth(ctx: ReportContext, ctx_kwargs_altimetry: dict):
     asp_dem = ctx.asp_dem
     sections: List[object] = []
 
-    # Parse --atl06sr_time_range into time_range/t0/t1 kwargs
+    # Parse --atl06sr-time-range into time_range/t0/t1 kwargs
     atl06sr_time_range = cfg.atl06sr_time_range
     atl06sr_time_kwargs = {}
     if atl06sr_time_range.lower() == "all":
@@ -632,7 +650,7 @@ def _build_altimetry_planetary(ctx: ReportContext, body: str):
             f"  1. Run: request_planetary_altimetry --dem {asp_dem} --email <your_email>\n"
             f"  2. Wait for the email with a download link\n"
             f"  3. Download and unzip the result\n"
-            f"  4. Re-run asp_report with: --altimetry_csv <path_to_pts_csv.csv>\n"
+            f"  4. Re-run asp_report with: --altimetry-csv <path_to_pts_csv.csv>\n"
             f"\nSkipping {instrument} altimetry plots.\n"
             f"{'='*60}\n"
         )
@@ -751,7 +769,7 @@ REPORT_SECTIONS: List[ReportSpec] = [
     ReportSpec("match_points", lambda ctx: True, _build_match_points),
     ReportSpec(
         "bundle_adjust",
-        lambda ctx: bool(ctx.config.bundle_adjust_directory),
+        lambda ctx: bool(ctx.config.bundle_adjust_prefix),
         _build_bundle_adjust,
     ),
     ReportSpec("disparity", lambda ctx: True, _build_disparity),
@@ -766,29 +784,13 @@ REPORT_SECTIONS: List[ReportSpec] = [
 # ---------------------------------------------------------------------------
 
 
-def _resolve_plot_altimetry(config: ReportConfig) -> bool:
-    """Resolve the deprecated --plot_icesat alias against --plot_altimetry."""
-    plot_altimetry = config.plot_altimetry
-    if config.plot_icesat is not None:
-        import warnings
-
-        warnings.warn(
-            "--plot_icesat is deprecated. Use --plot_altimetry instead.",
-            DeprecationWarning,
-            stacklevel=1,
-        )
-        plot_icesat = config.plot_icesat
-        # Convert Click string 'True'/'False' to bool
-        if isinstance(plot_icesat, str):
-            plot_icesat = plot_icesat.lower() not in ("false", "0", "no")
-        plot_altimetry = plot_icesat
-    return plot_altimetry
-
-
 def _setup_context(config: ReportConfig) -> ReportContext:
     """Resolve paths, projection, DEM metadata, and shared plotters."""
     directory = os.path.expanduser(config.directory)
     config.directory = directory
+    ba_directory, ba_stem = resolve_directory_or_prefix(
+        directory, config.bundle_adjust_prefix
+    )
     if config.reference_dem:
         config.reference_dem = os.path.expanduser(config.reference_dem)
     if config.altimetry_csv:
@@ -858,7 +860,7 @@ def _setup_context(config: ReportConfig) -> ReportContext:
                 print(f"\nUsing map projection from DEM: {map_crs}\n")
             except Exception as e:
                 print(
-                    f"\nError getting projection from DEM: {e}. Using default projection EPSG:4326. If you want a different projection, use the --map_crs flag.\n"
+                    f"\nError getting projection from DEM: {e}. Using default projection EPSG:4326. If you want a different projection, use the --map-crs flag.\n"
                 )
                 map_crs = "EPSG:4326"
 
@@ -875,10 +877,8 @@ def _setup_context(config: ReportConfig) -> ReportContext:
                 (float(valid.min()), float(valid.max())) if valid.size else (0, 0)
             )
             acq_extra_dirs = [os.path.join(directory, config.stereo_directory)]
-            if config.bundle_adjust_directory:
-                acq_extra_dirs.append(
-                    os.path.join(directory, config.bundle_adjust_directory)
-                )
+            if ba_directory:
+                acq_extra_dirs.append(os.path.join(directory, ba_directory))
             acquisition_dates = get_acquisition_dates(
                 directory, extra_dirs=acq_extra_dirs
             )
@@ -915,7 +915,9 @@ def _setup_context(config: ReportConfig) -> ReportContext:
         ctx_kwargs=ctx_kwargs,
         stereo_plotter=stereo_plotter,
         asp_dem=asp_dem,
-        plot_altimetry=_resolve_plot_altimetry(config),
+        plot_altimetry=config.plot_altimetry,
+        ba_directory=ba_directory,
+        ba_stem=ba_stem,
         report_metadata=report_metadata,
         reuse_clip_windows=reuse_clip_windows,
         reuse_clip_windows_crs=reuse_clip_windows_crs,
@@ -983,7 +985,8 @@ def run_report(config: ReportConfig) -> str:
     # Compile report
     processing_parameters = ProcessingParameters(
         processing_directory=config.directory,
-        bundle_adjust_directory=config.bundle_adjust_directory,
+        bundle_adjust_directory=ctx.ba_directory,
+        bundle_adjust_stem=ctx.ba_stem,
         stereo_directory=config.stereo_directory,
     )
     processing_parameters_dict = processing_parameters.from_log_files()

{asp_plot-2.2.0 → asp_plot-3.0.0}/asp_plot/utils.py

@@ -84,6 +84,42 @@ def glob_file(directory, *patterns, all_files=False, recursive=False, quiet=Fals
     return None
 
 
+def resolve_directory_or_prefix(base_directory, value):
+    """
+    Resolve a CLI value that may name a directory or an ASP output prefix.
+
+    ASP tools take output *prefixes* (``--bundle-adjust-prefix ba/run``), while
+    asp_plot historically took the containing *directory* (``ba``). This
+    accepts both: an existing directory is returned as-is with no stem, while
+    a prefix is split into its directory and run stem so file globs can be
+    narrowed to that run (``run-final_residuals_pointmap.csv``).
+
+    Parameters
+    ----------
+    base_directory : str
+        Directory the value is relative to (the report's ``--directory``).
+    value : str or None
+        Directory or prefix, relative to ``base_directory``. Trailing slashes
+        are stripped.
+
+    Returns
+    -------
+    tuple of (str or None, str or None)
+        ``(subdirectory, stem)``; ``stem`` is None when ``value`` names a
+        directory. A separator-free value that is not an existing directory is
+        kept as a directory so downstream "not found" errors point at it.
+    """
+    if value is None:
+        return None, None
+    value = value.rstrip("/\\")
+    if os.path.isdir(os.path.join(os.path.expanduser(base_directory), value)):
+        return value, None
+    subdirectory, stem = os.path.split(value)
+    if subdirectory and stem:
+        return subdirectory, stem
+    return value, None
+
+
 def find_pair_directories(directory):
     """
     Find the per-pair subdirectories of an ASP multi-view stereo run.

{asp_plot-2.2.0 → asp_plot-3.0.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "asp_plot"
-version = "2.2.0"
+version = "3.0.0"
 license = {text = "BSD-3-Clause"}
 authors = [
   { name="Ben Purinton", email="purinton@uw.edu" },