Add CLI flag for choosing recon filename stem

docs/source/howto/run_httomo.rst

@@ -183,6 +183,8 @@ The :code:`run` command
                                       Number of frames per-chunk in intermediate
                                       data (0 = write as contiguous, -1 = decide
                                       automatically)  [x>=-1]
+      --recon-filename-stem TEXT      Name of output recon file without file
+                                      extension (assumes `.h5`)
       --help                          Show this message and exit.
 
 Arguments
@@ -224,7 +226,7 @@ directory created by HTTomo would be
 Options/flags
 #############
 
-The :code:`run` command has 13 options/flags:
+The :code:`run` command has 14 options/flags:
 
 - :code:`--output-folder-name`
 - :code:`--save-all`
@@ -239,6 +241,7 @@ The :code:`run` command has 13 options/flags:
 - :code:`--syslog-host`
 - :code:`--syslog-port`
 - :code:`--frames-per-chunk`
+- :code:`--recon-filename-stem`
 
 :code:`--output-folder-name`
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -448,3 +451,23 @@ This flag sets the number of frames in a chunk for the intermediate file.
 For most cases the default -1 should be sufficient as the actual number of
 frames in a chunk is optimised by considering the saturation bandwidth of the
 filesystem.
+
+:code:`--recon-filename-stem`
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+By default, if the output of a method is saved to a file, the filename is of
+the form :code:`task_{N}-{PACKAGE_NAME}-{METHOD_NAME}.h5`, where:
+
+- :code:`N` is the index of the method in the pipeline (zero-indexing)
+- :code:`PACKAGE_NAME` is the name of the package that the method comes from
+- :code:`METHOD_NAME` is the name of the method
+
+For the output of a reconstruction method specifically, if a filename different
+to the above format is desired, this can be provided using the
+:code:`--recon-filename-stem` flag. The files created will always be hdf5
+files, so the file extension should always be :code:`h5`. Therefore, only the
+"stem" of the desired filename needs to be provided (the part of the filename
+before the file extension).
+
+For example, if the desired reconstruction filename is :code:`my-recon.h5`,
+then the flag should be used as :code:`--recon-filename-stem=my-recon`.

httomo/cli.py

@@ -144,6 +144,12 @@ def check(yaml_config: Path, in_data_file: Optional[Path] = None):
         "(0 = write as contiguous, -1 = decide automatically)"
     ),
 )
+@click.option(
+    "--recon-filename-stem",
+    type=click.STRING,
+    default=None,
+    help="Name of output recon file without file extension (assumes `.h5`)",
+)
 def run(
     in_data_file: Path,
     yaml_config: Path,
@@ -161,6 +167,7 @@ def run(
     syslog_host: str,
     syslog_port: int,
     frames_per_chunk: int,
+    recon_filename_stem: Optional[str],
 ):
     """Run a pipeline defined in YAML on input data."""
     set_global_constants(
@@ -172,6 +179,7 @@ def run(
         syslog_host,
         syslog_port,
         output_folder_name,
+        recon_filename_stem,
     )
 
     does_contain_sweep = is_sweep_pipeline(yaml_config)
@@ -250,6 +258,7 @@ def set_global_constants(
     syslog_host: str,
     syslog_port: int,
     output_folder_name: Optional[Path],
+    recon_filename_stem: Optional[str],
 ) -> None:
     if compress_intermediate and frames_per_chunk == 0:
         # 0 means write contiguously but compression must have chunk
@@ -260,6 +269,7 @@ def set_global_constants(
     httomo.globals.FRAMES_PER_CHUNK = frames_per_chunk
     httomo.globals.SYSLOG_SERVER = syslog_host
     httomo.globals.SYSLOG_PORT = syslog_port
+    httomo.globals.RECON_FILENAME_STEM = recon_filename_stem
 
     if output_folder_name is None:
         httomo.globals.run_out_dir = out_dir.joinpath(

httomo/globals.py

@@ -1,5 +1,6 @@
 import os
 from pathlib import Path
+from typing import Optional
 
 run_out_dir: os.PathLike = Path(".")
 gpu_id: int = -1
@@ -14,3 +15,4 @@
 COMPRESS_INTERMEDIATE: bool = False
 SYSLOG_SERVER = "localhost"
 SYSLOG_PORT = 514
+RECON_FILENAME_STEM: Optional[str] = None

httomo/method_wrappers/save_intermediate.py

@@ -47,8 +47,11 @@ def __init__(
         assert prev_method is not None
 
         filename = f"{prev_method.task_id}-{prev_method.package_name}-{prev_method.method_name}"
-        if prev_method.recon_algorithm is not None:
+        is_saving_recon = prev_method.module_path.endswith(".algorithm")
+        if is_saving_recon and prev_method.recon_algorithm is not None:
             filename += f"-{prev_method.recon_algorithm}"
+        if is_saving_recon and httomo.globals.RECON_FILENAME_STEM is not None:
+            filename = httomo.globals.RECON_FILENAME_STEM
 
         if out_dir is None:
             out_dir = httomo.globals.run_out_dir

tests/method_wrappers/test_save_intermediate.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import List, Tuple
+from typing import Callable, List, Optional, Tuple
 from unittest import mock
 import pytest
 from pytest_mock import MockerFixture
@@ -278,3 +278,137 @@ def save_intermediate_data(
     # Execute the padded block with the intermediate wrapper and let the assertions in the
     # dummy method function run the appropriate checks
     wrp.execute(block)
+
+
+@pytest.mark.parametrize("recon_filename_stem_global_var", [None, "some-recon"])
+@pytest.mark.parametrize(
+    "recon_algorithm",
+    [None, "gridrec"],
+    ids=["specify-recon-algorithm", "dont-specify-recon-algorithm"],
+)
+def test_recon_method_output_filename(
+    get_files: Callable,
+    mocker: MockerFixture,
+    tmp_path: Path,
+    recon_filename_stem_global_var: Optional[str],
+    recon_algorithm: Optional[str],
+):
+    httomo.globals.RECON_FILENAME_STEM = recon_filename_stem_global_var
+    loader: LoaderInterface = mocker.create_autospec(
+        LoaderInterface, instance=True, detector_x=10, detector_y=20
+    )
+
+    class FakeModule:
+        def save_intermediate_data(
+            data,
+            global_shape: Tuple[int, int, int],
+            global_index: Tuple[int, int, int],
+            slicing_dim: int,
+            file: h5py.File,
+            frames_per_chunk: int,
+            path: str,
+            detector_x: int,
+            detector_y: int,
+            angles: np.ndarray,
+        ):
+            pass
+
+    mocker.patch(
+        "httomo.method_wrappers.generic.import_module", return_value=FakeModule
+    )
+    TASK_ID = "task1"
+    PACKAGE_NAME = "testpackage"
+    METHOD_NAME = "testreconmethod"
+    MODULE_PATH = f"{PACKAGE_NAME}.algorithm"
+    if recon_filename_stem_global_var is None and recon_algorithm is None:
+        expected_filename = f"{TASK_ID}-{PACKAGE_NAME}-{METHOD_NAME}"
+    if recon_filename_stem_global_var is None and recon_algorithm is not None:
+        expected_filename = f"{TASK_ID}-{PACKAGE_NAME}-{METHOD_NAME}-{recon_algorithm}"
+    if recon_filename_stem_global_var is not None:
+        expected_filename = recon_filename_stem_global_var
+    expected_filename += ".h5"
+    prev_method = mocker.create_autospec(
+        MethodWrapper,
+        instance=True,
+        task_id=TASK_ID,
+        package_name=PACKAGE_NAME,
+        method_name=METHOD_NAME,
+        module_path=MODULE_PATH,
+        recon_algorithm=recon_algorithm,
+    )
+    mocker.patch.object(httomo.globals, "run_out_dir", tmp_path)
+    wrp = make_method_wrapper(
+        make_mock_repo(mocker, implementation="cpu"),
+        "httomo.methods",
+        "save_intermediate_data",
+        MPI.COMM_WORLD,
+        make_mock_preview_config(mocker),
+        loader=loader,
+        prev_method=prev_method,
+    )
+
+    assert isinstance(wrp, SaveIntermediateFilesWrapper)
+    files = get_files(tmp_path)
+    assert len(files) == 1
+    assert Path(files[0]).name == expected_filename
+
+
+@pytest.mark.parametrize("recon_filename_stem_global_var", [None, "some-recon"])
+def test_non_recon_method_output_filename(
+    get_files: Callable,
+    mocker: MockerFixture,
+    tmp_path: Path,
+    recon_filename_stem_global_var: Optional[str],
+):
+    httomo.globals.RECON_FILENAME_STEM = recon_filename_stem_global_var
+    loader: LoaderInterface = mocker.create_autospec(
+        LoaderInterface, instance=True, detector_x=10, detector_y=20
+    )
+
+    class FakeModule:
+        def save_intermediate_data(
+            data,
+            global_shape: Tuple[int, int, int],
+            global_index: Tuple[int, int, int],
+            slicing_dim: int,
+            file: h5py.File,
+            frames_per_chunk: int,
+            path: str,
+            detector_x: int,
+            detector_y: int,
+            angles: np.ndarray,
+        ):
+            pass
+
+    mocker.patch(
+        "httomo.method_wrappers.generic.import_module", return_value=FakeModule
+    )
+    TASK_ID = "task1"
+    PACKAGE_NAME = "testpackage"
+    METHOD_NAME = "testmethod"
+    MODULE_PATH = f"{PACKAGE_NAME}.notalgorithm"
+    EXPECTED_FILENAME = f"{TASK_ID}-{PACKAGE_NAME}-{METHOD_NAME}.h5"
+    prev_method = mocker.create_autospec(
+        MethodWrapper,
+        instance=True,
+        task_id=TASK_ID,
+        package_name=PACKAGE_NAME,
+        method_name=METHOD_NAME,
+        module_path=MODULE_PATH,
+        recon_algorithm=None,
+    )
+    mocker.patch.object(httomo.globals, "run_out_dir", tmp_path)
+    wrp = make_method_wrapper(
+        make_mock_repo(mocker, implementation="cpu"),
+        "httomo.methods",
+        "save_intermediate_data",
+        MPI.COMM_WORLD,
+        make_mock_preview_config(mocker),
+        loader=loader,
+        prev_method=prev_method,
+    )
+
+    assert isinstance(wrp, SaveIntermediateFilesWrapper)
+    files = get_files(tmp_path)
+    assert len(files) == 1
+    assert Path(files[0]).name == EXPECTED_FILENAME

tests/test_cli.py

@@ -84,5 +84,37 @@ def test_output_folder_name_correctly_sets_run_out_dir_global_constant(output_fo
         syslog_host="localhost",
         syslog_port=514,
         output_folder_name=Path(dir_name),
+        recon_filename_stem=None,
     )
     assert httomo.globals.run_out_dir == custom_output_dir
+
+
+@pytest.mark.parametrize(
+    "use_recon_filename_stem_flag",
+    [True, False],
+)
+def test_cli_recon_filename_stem_flag(
+    standard_data, standard_loader, output_folder, use_recon_filename_stem_flag: bool
+):
+    runner = CliRunner()
+    if use_recon_filename_stem_flag:
+        filename_stem = "my-file"
+        runner.invoke(
+            main,
+            [
+                "run",
+                standard_data,
+                standard_loader,
+                output_folder,
+                "--recon-filename-stem",
+                filename_stem,
+            ],
+        )
+        assert httomo.globals.RECON_FILENAME_STEM is not None
+        assert httomo.globals.RECON_FILENAME_STEM == filename_stem
+    else:
+        runner.invoke(
+            main,
+            ["run", standard_data, standard_loader, output_folder],
+        )
+        assert httomo.globals.RECON_FILENAME_STEM is None