RF: from tff_* to trx_* => rename CLI

README.md

@@ -41,28 +41,28 @@ save(trx, "output.trk")
 
 ### Command-Line Interface
 
-TRX-Python provides a unified CLI (`tff`) for common operations:
+TRX-Python provides a unified CLI (`trx`) for common operations:
 
 ```bash
 # Show all available commands
-tff --help
+trx --help
 
 # Convert between formats
-tff convert input.trk output.trx
+trx convert input.trk output.trx
 
 # Concatenate tractograms
-tff concatenate tract1.trx tract2.trx merged.trx
+trx concatenate tract1.trx tract2.trx merged.trx
 
 # Validate a TRX file
-tff validate data.trx
+trx validate data.trx
 ```
 
 Individual commands are also available for backward compatibility:
 
 ```bash
-tff_convert_tractogram input.trk output.trx
-tff_concatenate_tractograms tract1.trx tract2.trx merged.trx
-tff_validate_trx data.trx
+trx_convert_tractogram input.trk output.trx
+trx_concatenate_tractograms tract1.trx tract2.trx merged.trx
+trx_validate data.trx
 ```
 
 ## Development

docs/source/scripts.rst

@@ -3,38 +3,38 @@
 Command-line Interface
 ======================
 
-The TRX toolkit provides a unified command-line interface ``tff`` as well as individual standalone commands for backward compatibility. All commands become available on your ``PATH`` after installing ``trx-python``.
+The TRX toolkit provides a unified command-line interface ``trx`` as well as individual standalone commands for backward compatibility. All commands become available on your ``PATH`` after installing ``trx-python``.
 
 Each command supports ``--help`` for full options.
 
-Unified CLI: ``tff``
+Unified CLI: ``trx``
 --------------------
 
-The recommended way to use TRX commands is through the unified ``tff`` CLI:
+The recommended way to use TRX commands is through the unified ``trx`` CLI:
 
 .. code-block:: bash
 
-    tff --help              # Show all available commands
-    tff <command> --help    # Show help for a specific command
+    trx --help              # Show all available commands
+    trx <command> --help    # Show help for a specific command
 
 Available subcommands:
 
-- ``tff concatenate`` - Concatenate multiple tractograms
-- ``tff convert`` - Convert between tractography formats
-- ``tff convert-dsi`` - Fix DSI-Studio TRK files
-- ``tff generate`` - Generate TRX from raw data files
-- ``tff manipulate-dtype`` - Change array data types
-- ``tff compare`` - Simple tractogram comparison
-- ``tff validate`` - Validate and clean TRX files
-- ``tff verify-header`` - Check header compatibility
-- ``tff visualize`` - Visualize tractogram overlap
+- ``trx concatenate`` - Concatenate multiple tractograms
+- ``trx convert`` - Convert between tractography formats
+- ``trx convert-dsi`` - Fix DSI-Studio TRK files
+- ``trx generate`` - Generate TRX from raw data files
+- ``trx manipulate-dtype`` - Change array data types
+- ``trx compare`` - Simple tractogram comparison
+- ``trx validate`` - Validate and clean TRX files
+- ``trx verify-header`` - Check header compatibility
+- ``trx visualize`` - Visualize tractogram overlap
 
 Standalone Commands
 -------------------
 
 For backward compatibility, standalone commands are also available:
 
-tff_concatenate_tractograms
+trx_concatenate_tractograms
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Concatenate multiple tractograms into a single output.
 
@@ -44,24 +44,24 @@ Concatenate multiple tractograms into a single output.
 .. code-block:: bash
 
     # Using unified CLI
-    tff concatenate in1.trk in2.trk merged.trx
+    trx concatenate in1.trk in2.trk merged.trx
 
     # Using standalone command
-    tff_concatenate_tractograms in1.trk in2.trk merged.trx
+    trx_concatenate_tractograms in1.trk in2.trk merged.trx
 
-tff_convert_dsi_studio
+trx_convert_dsi_studio
 ~~~~~~~~~~~~~~~~~~~~~~
 Convert a DSI Studio ``.trk`` with accompanying ``.nii.gz`` reference into a cleaned ``.trk`` or TRX.
 
 .. code-block:: bash
 
     # Using unified CLI
-    tff convert-dsi input.trk reference.nii.gz cleaned.trk
+    trx convert-dsi input.trk reference.nii.gz cleaned.trk
 
     # Using standalone command
-    tff_convert_dsi_studio input.trk reference.nii.gz cleaned.trk
+    trx_convert_dsi_studio input.trk reference.nii.gz cleaned.trk
 
-tff_convert_tractogram
+trx_convert_tractogram
 ~~~~~~~~~~~~~~~~~~~~~~
 General-purpose converter between ``trk``, ``tck``, ``vtk``, ``fib``, ``dpy``, and ``trx``.
 
@@ -70,26 +70,26 @@ General-purpose converter between ``trk``, ``tck``, ``vtk``, ``fib``, ``dpy``, a
 .. code-block:: bash
 
     # Using unified CLI
-    tff convert input.trk output.trx --positions-dtype float32 --offsets-dtype uint64
+    trx convert input.trk output.trx --positions-dtype float32 --offsets-dtype uint64
 
     # Using standalone command
-    tff_convert_tractogram input.trk output.trx --positions-dtype float32 --offsets-dtype uint64
+    trx_convert_tractogram input.trk output.trx --positions-dtype float32 --offsets-dtype uint64
 
-tff_generate_trx_from_scratch
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+trx_generate_from_scratch
+~~~~~~~~~~~~~~~~~~~~~~~~~
 Build a TRX file from raw NumPy arrays or CSV streamline coordinates.
 
 - Flags: ``--positions``, ``--offsets``, ``--positions-dtype``, ``--offsets-dtype``, spatial options (``--space``, ``--origin``), and metadata loaders for dpv/dps/groups/dpg.
 
 .. code-block:: bash
 
     # Using unified CLI
-    tff generate fa.nii.gz output.trx --positions positions.npy --offsets offsets.npy
+    trx generate fa.nii.gz output.trx --positions positions.npy --offsets offsets.npy
 
     # Using standalone command
-    tff_generate_trx_from_scratch fa.nii.gz output.trx --positions positions.npy --offsets offsets.npy
+    trx_generate_from_scratch fa.nii.gz output.trx --positions positions.npy --offsets offsets.npy
 
-tff_manipulate_datatype
+trx_manipulate_datatype
 ~~~~~~~~~~~~~~~~~~~~~~~
 Rewrite TRX datasets with new dtypes for positions/offsets/dpv/dps/dpg/groups.
 
@@ -98,61 +98,61 @@ Rewrite TRX datasets with new dtypes for positions/offsets/dpv/dps/dpg/groups.
 .. code-block:: bash
 
     # Using unified CLI
-    tff manipulate-dtype input.trx output.trx --positions-dtype float16 --dpv color,uint8
+    trx manipulate-dtype input.trx output.trx --positions-dtype float16 --dpv color,uint8
 
     # Using standalone command
-    tff_manipulate_datatype input.trx output.trx --positions-dtype float16 --dpv color,uint8
+    trx_manipulate_datatype input.trx output.trx --positions-dtype float16 --dpv color,uint8
 
-tff_simple_compare
+trx_simple_compare
 ~~~~~~~~~~~~~~~~~~
 Compare two tractograms for quick difference checks.
 
 .. code-block:: bash
 
     # Using unified CLI
-    tff compare first.trk second.trk
+    trx compare first.trk second.trk
 
     # Using standalone command
-    tff_simple_compare first.trk second.trk
+    trx_simple_compare first.trk second.trk
 
-tff_validate_trx
-~~~~~~~~~~~~~~~~
+trx_validate
+~~~~~~~~~~~~
 Validate a TRX file for consistency and remove invalid streamlines.
 
 .. code-block:: bash
 
     # Using unified CLI
-    tff validate data.trx --out cleaned.trx
+    trx validate data.trx --out cleaned.trx
 
     # Using standalone command
-    tff_validate_trx data.trx --out cleaned.trx
+    trx_validate data.trx --out cleaned.trx
 
-tff_verify_header_compatibility
+trx_verify_header_compatibility
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Check whether tractogram headers are compatible for operations such as concatenation.
 
 .. code-block:: bash
 
     # Using unified CLI
-    tff verify-header file1.trk file2.trk
+    trx verify-header file1.trk file2.trk
 
     # Using standalone command
-    tff_verify_header_compatibility file1.trk file2.trk
+    trx_verify_header_compatibility file1.trk file2.trk
 
-tff_visualize_overlap
+trx_visualize_overlap
 ~~~~~~~~~~~~~~~~~~~~~
 Visualize streamline overlap between tractograms (requires visualization dependencies).
 
 .. code-block:: bash
 
     # Using unified CLI
-    tff visualize tractogram.trk reference.nii.gz
+    trx visualize tractogram.trk reference.nii.gz
 
     # Using standalone command
-    tff_visualize_overlap tractogram.trk reference.nii.gz
+    trx_visualize_overlap tractogram.trk reference.nii.gz
 
 Notes
 -----
 - Test datasets for examples can be fetched with ``python -m trx.fetcher`` helpers: ``fetch_data(get_testing_files_dict())`` downloads to ``$TRX_HOME`` (default ``~/.tee_ar_ex``).
 - All commands print detailed usage with ``--help``.
-- The unified ``tff`` CLI uses `Typer <https://typer.tiangolo.com/>`_ for beautiful terminal output with colors and rich formatting.
+- The unified ``trx`` CLI uses `Typer <https://typer.tiangolo.com/>`_ for beautiful terminal output with colors and rich formatting.

pyproject.toml

@@ -70,16 +70,16 @@ Documentation = "https://tee-ar-ex.github.io/trx-python/"
 Repository = "https://github.com/tee-ar-ex/trx-python"
 
 [project.scripts]
-tff = "trx.cli:main"
-tff_concatenate_tractograms = "trx.cli:concatenate_tractograms_cmd"
-tff_convert_dsi_studio = "trx.cli:convert_dsi_cmd"
-tff_convert_tractogram = "trx.cli:convert_cmd"
-tff_generate_trx_from_scratch = "trx.cli:generate_cmd"
-tff_manipulate_datatype = "trx.cli:manipulate_dtype_cmd"
-tff_simple_compare = "trx.cli:compare_cmd"
-tff_validate_trx = "trx.cli:validate_cmd"
-tff_verify_header_compatibility = "trx.cli:verify_header_cmd"
-tff_visualize_overlap = "trx.cli:visualize_cmd"
+trx = "trx.cli:main"
+trx_concatenate_tractograms = "trx.cli:concatenate_tractograms_cmd"
+trx_convert_dsi_studio = "trx.cli:convert_dsi_cmd"
+trx_convert_tractogram = "trx.cli:convert_cmd"
+trx_generate_from_scratch = "trx.cli:generate_cmd"
+trx_manipulate_datatype = "trx.cli:manipulate_dtype_cmd"
+trx_simple_compare = "trx.cli:compare_cmd"
+trx_validate = "trx.cli:validate_cmd"
+trx_verify_header_compatibility = "trx.cli:verify_header_cmd"
+trx_visualize_overlap = "trx.cli:visualize_cmd"
 
 [tool.setuptools]
 packages = ["trx"]

trx/cli.py

@@ -26,7 +26,7 @@
 )
 
 app = typer.Typer(
-    name="tff",
+    name="trx",
     help="TRX File Format Tools - CLI for brain tractography data manipulation.",
     add_completion=False,
     rich_markup_mode="rich",
@@ -758,55 +758,55 @@ def _create_standalone_app(command_func, name: str, help_text: str):
 
 concatenate_tractograms_cmd = _create_standalone_app(
     concatenate_tractograms,
-    "tff_concatenate_tractograms",
+    "trx_concatenate_tractograms",
     "Concatenate multiple tractograms into one.",
 )
 
 convert_dsi_cmd = _create_standalone_app(
     convert_dsi,
-    "tff_convert_dsi_studio",
+    "trx_convert_dsi_studio",
     "Fix DSI-Studio TRK files for compatibility.",
 )
 
 convert_cmd = _create_standalone_app(
     convert,
-    "tff_convert_tractogram",
+    "trx_convert_tractogram",
     "Convert tractograms between formats.",
 )
 
 generate_cmd = _create_standalone_app(
     generate,
-    "tff_generate_trx_from_scratch",
+    "trx_generate_from_scratch",
     "Generate TRX file from raw data files.",
 )
 
 manipulate_dtype_cmd = _create_standalone_app(
     manipulate_dtype,
-    "tff_manipulate_datatype",
+    "trx_manipulate_datatype",
     "Manipulate TRX file internal array data types.",
 )
 
 compare_cmd = _create_standalone_app(
     compare,
-    "tff_simple_compare",
+    "trx_simple_compare",
     "Simple comparison of tractograms by subtracting coordinates.",
 )
 
 validate_cmd = _create_standalone_app(
     validate,
-    "tff_validate_trx",
+    "trx_validate",
     "Validate TRX file and remove invalid streamlines.",
 )
 
 verify_header_cmd = _create_standalone_app(
     verify_header,
-    "tff_verify_header_compatibility",
+    "trx_verify_header_compatibility",
     "Compare spatial attributes of input files.",
 )
 
 visualize_cmd = _create_standalone_app(
     visualize,
-    "tff_visualize_overlap",
+    "trx_visualize_overlap",
     "Display tractogram and density map with bounding box.",
 )