REF: Remove viz module leftovers

docs/source/dev.md

@@ -268,7 +268,6 @@ trx-python/
 │   ├── streamlines_ops.py  # Streamline operations
 │   ├── trx_file_memmap.py  # Core TrxFile class
 │   ├── utils.py            # Utility functions
-│   ├── viz.py              # Visualization (optional)
 │   ├── workflows.py        # High-level workflows
 │   └── tests/              # Test suite
 ├── docs/                   # Documentation

trx/cli.py

@@ -19,7 +19,6 @@
     generate_trx_from_scratch,
     manipulate_trx_datatype,
     tractogram_simple_compare,
-    tractogram_visualize_overlap,
     validate_tractogram,
     verify_header_compatibility,
 )
@@ -920,47 +919,6 @@ def verify_header(
     verify_header_compatibility([str(f) for f in in_files])
 
 
-@app.command("visualize")
-def visualize(
-    in_tractogram: Annotated[
-        Path,
-        typer.Argument(help="Input tractogram. Format: trk, tck, vtk, fib, dpy, trx."),
-    ],
-    reference: Annotated[
-        Path,
-        typer.Argument(help="Reference anatomy (.nii or .nii.gz)."),
-    ],
-    remove_invalid: Annotated[
-        bool,
-        typer.Option(
-            "--remove-invalid",
-            help="Remove invalid streamlines to avoid density_map crash.",
-        ),
-    ] = False,
-) -> None:
-    """Display tractogram and density map with bounding box.
-
-    Parameters
-    ----------
-    in_tractogram : Path
-        Input tractogram (.trk, .tck, .vtk, .fib, .dpy, .trx).
-    reference : Path
-        Reference anatomy (.nii or .nii.gz).
-    remove_invalid : bool, optional
-        Remove invalid streamlines to avoid density map crashes.
-
-    Returns
-    -------
-    None
-        Opens visualization windows when fury is available.
-    """
-    tractogram_visualize_overlap(
-        str(in_tractogram),
-        str(reference),
-        remove_invalid,
-    )
-
-
 def _format_size(size_bytes: int) -> str:
     """Format byte size to human readable string.
 
@@ -1150,12 +1108,6 @@ def _create_standalone_app(command_func, name: str, help_text: str):
     "Compare spatial attributes of input files.",
 )
 
-visualize_cmd = _create_standalone_app(
-    visualize,
-    "trx_visualize_overlap",
-    "Display tractogram and density map with bounding box.",
-)
-
 info_cmd = _create_standalone_app(
     info,
     "trx_info",

trx/tests/test_cli.py

@@ -90,10 +90,6 @@ def test_help_option_verify_header(self, script_runner):
         ret = script_runner.run(["trx_verify_header_compatibility", "--help"])
         assert ret.success
 
-    def test_help_option_visualize(self, script_runner):
-        ret = script_runner.run(["trx_visualize_overlap", "--help"])
-        assert ret.success
-
     def test_help_option_info(self, script_runner):
         ret = script_runner.run(["trx_info", "--help"])
         assert ret.success
@@ -139,10 +135,6 @@ def test_trx_verify_header_help(self, script_runner):
         ret = script_runner.run(["trx", "verify-header", "--help"])
         assert ret.success
 
-    def test_trx_visualize_help(self, script_runner):
-        ret = script_runner.run(["trx", "visualize", "--help"])
-        assert ret.success
-
     def test_trx_info_help(self, script_runner):
         ret = script_runner.run(["trx", "info", "--help"])
         assert ret.success

trx/workflows.py

@@ -9,7 +9,6 @@
 import os
 import tempfile
 
-import nibabel as nib
 from nibabel.streamlines.array_sequence import ArraySequence
 import numpy as np
 
@@ -32,7 +31,6 @@
     load_matrix_in_any_format,
     split_name_with_gz,
 )
-from trx.viz import display
 
 
 def convert_dsi_studio(
@@ -273,81 +271,6 @@ def verify_header_compatibility(in_files):
         print("All input files have compatible headers.")
 
 
-def tractogram_visualize_overlap(in_tractogram, reference, remove_invalid=True):
-    """Visualize overlap between tractogram density maps in different spaces.
-
-    Parameters
-    ----------
-    in_tractogram : str
-        Input tractogram path.
-    reference : str
-        Reference anatomy (.nii or .nii.gz).
-    remove_invalid : bool, optional
-        Remove streamlines outside bounding box before visualization.
-
-    Returns
-    -------
-    None
-        Opens interactive windows when fury is available.
-    """
-    if not dipy_available:
-        logging.error("Dipy library is missing, scripts are not available.")
-        return None
-    from dipy.io.stateful_tractogram import StatefulTractogram
-    from dipy.tracking.streamline import set_number_of_points
-    from dipy.tracking.utils import density_map
-
-    tractogram_obj = load(in_tractogram, reference)
-    if not isinstance(tractogram_obj, StatefulTractogram):
-        sft = tractogram_obj.to_sft()
-        tractogram_obj.close()
-    else:
-        sft = tractogram_obj
-    sft.streamlines._data = sft.streamlines._data.astype(float)
-
-    sft.data_per_point = None
-    sft.streamlines = set_number_of_points(sft.streamlines, 200)
-
-    if remove_invalid:
-        sft.remove_invalid_streamlines()
-
-    # Approach (1)
-    density_1 = density_map(sft.streamlines, sft.affine, sft.dimensions)
-    img = nib.load(reference)
-    display(
-        img.get_fdata(),
-        volume_affine=img.affine,
-        streamlines=sft.streamlines,
-        title="RASMM",
-    )
-
-    # Approach (2)
-    sft.to_vox()
-    density_2 = density_map(sft.streamlines, np.eye(4), sft.dimensions)
-
-    # Small difference due to casting of the affine as float32 or float64
-    diff = density_1 - density_2
-    print(
-        "Total difference of {} voxels with total value of {}".format(
-            np.count_nonzero(diff), np.sum(np.abs(diff))
-        )
-    )
-
-    display(img.get_fdata(), streamlines=sft.streamlines, title="VOX")
-
-    # Try VOXMM
-    sft.to_voxmm()
-    affine = np.eye(4)
-    affine[0:3, 0:3] *= sft.voxel_sizes
-
-    display(
-        img.get_fdata(),
-        volume_affine=affine,
-        streamlines=sft.streamlines,
-        title="VOXMM",
-    )
-
-
 def validate_tractogram(
     in_tractogram,
     reference,