Merge branch 'main' into prep-1.0.0rc1

.circleci/config.yml

@@ -702,6 +702,8 @@ workflows:
             - Recon_PYAFQExternalTrk
             - Recon_ScalarMap
             - Recon_multises_pre1_IO_test
+            - Recon_multises_post1_IO_test
+            - Recon_msmt_Multishell_HSVS
           filters:
             branches:
               ignore:

qsirecon/cli/recon_plot.py

@@ -101,7 +101,6 @@ def recon_plot():
     parser.add_argument("--padding", type=int, default=10, help="number of slices to plot")
     opts = parser.parse_args()
 
-    print(f"TMPDIR={os.getenv('TMPDIR')}")
     if opts.mif:
         odf_img, directions = mif2amps(opts.mif, os.getcwd())
         LOGGER.info("converting %s to plot ODF/peaks", opts.mif)
@@ -126,29 +125,65 @@ def recon_plot():
     else:
         background_data = nb.load(opts.background_image).get_fdata()
 
-    LOGGER.info("saving peaks image to %s", opts.peaks_image)
-    peak_slice_series(
-        odf_4d,
-        sphere,
-        background_data,
-        opts.peaks_image,
-        n_cuts=opts.ncuts,
-        mask_image=opts.mask_file,
-        padding=opts.padding,
-    )
+    LOGGER.info("Starting a virtual framebuffer for FURY")
 
-    # Plot ODFs in interesting regions
-    if opts.odf_rois and not opts.peaks_only:
-        LOGGER.info("saving odfs image to %s", opts.odfs_image)
-        odf_roi_plot(
+    # Xvfb won't allow an empty $DISPLAY
+    if "DISPLAY" in os.environ:
+        del os.environ["DISPLAY"]
+
+    from xvfbwrapper import Xvfb
+
+    display = Xvfb(nolisten="tcp")
+    display.extra_xvfb_args += ["+iglx"]
+
+    try:
+        display.start()
+    except Exception as exc:
+        LOGGER.warning(
+            "Unable to start Xvfb!! If you are running this via Apptainer/Singularity "
+            "there may be an issue accessing the /tmp directory.\n\n"
+            "If you used the --containall flag, please also use --writable-tmpfs.\n\n"
+            "Otherwise, be sure that the /tmp directory is writable by Singularity/Apptainer. "
+            "This may require contacting a system administrator.\n\n"
+            f"The python error was\n{exc}"
+        )
+        sys.exit(1)
+
+    try:
+        peak_slice_series(
             odf_4d,
             sphere,
             background_data,
-            opts.odfs_image,
-            opts.odf_rois,
-            subtract_iso=opts.subtract_iso,
-            mask=opts.mask_file,
+            opts.peaks_image,
+            n_cuts=opts.ncuts,
+            mask_image=opts.mask_file,
+            padding=opts.padding,
         )
+    except Exception as exc:
+        LOGGER.warning(exc)
+        sys.exit(1)
+
+    LOGGER.info("saving peaks image to %s", opts.peaks_image)
+
+    # Plot ODFs in interesting regions
+    if opts.odf_rois and not opts.peaks_only:
+        try:
+            odf_roi_plot(
+                odf_4d,
+                sphere,
+                background_data,
+                opts.odfs_image,
+                opts.odf_rois,
+                subtract_iso=opts.subtract_iso,
+                mask=opts.mask_file,
+            )
+        except Exception as exc:
+            LOGGER.warning(exc)
+            sys.exit(1)
+
+        LOGGER.info("saved odfs image to %s", opts.odfs_image)
+
+    display.stop()
     sys.exit(0)
 
 

qsirecon/config.py

@@ -537,7 +537,9 @@ def _process_value(value):
 
         cls._processing_list = []
         for dwi_relpath, anat_relpath in cls.processing_list:
-            cls._processing_list.append((cls.layout.get_file(dwi_relpath), cls.layout.get_file(anat_relpath)))
+            cls._processing_list.append(
+                (cls.layout.get_file(dwi_relpath), cls.layout.get_file(anat_relpath))
+            )
         cls.processing_list = cls._processing_list
 
         dataset_links = {

qsirecon/interfaces/reports.py

@@ -282,7 +282,6 @@ class CLIReconPeaksReport(CommandLine):
     input_spec = _ReconPeaksReportInputSpec
     output_spec = _ReconPeaksReportOutputSpec
     _cmd = "recon_plot"
-    _redirect_x = True
 
     def _list_outputs(self):
         outputs = self.output_spec().get()

qsirecon/tests/test_cli.py

@@ -9,14 +9,19 @@
 
 from qsirecon.cli import run
 from qsirecon.cli.parser import parse_args
-from qsirecon.cli.workflow import build_boilerplate, build_workflow
+from qsirecon.cli.workflow import build_boilerplate, build_workflow, copy_boilerplate
 from qsirecon.reports.core import generate_reports
 from qsirecon.tests.utils import (
     check_generated_files,
     download_test_data,
+    freesurfer_license,
     get_test_data_path,
 )
-from qsirecon.utils.bids import write_derivative_description
+from qsirecon.utils.bids import (
+    write_atlas_dataset_description,
+    write_bidsignore,
+    write_derivative_description,
+)
 
 nipype_config.enable_debug_mode()
 
@@ -58,7 +63,7 @@ def test_mrtrix_singleshell_ss3t_act(data_dir, output_dir, working_dir):
         "Gordon333Ext",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -95,7 +100,7 @@ def test_mrtrix_multishell_msmt_hsvs(data_dir, output_dir, working_dir):
         "--report-output-level=root",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -136,7 +141,7 @@ def test_mrtrix_singleshell_ss3t_noact(data_dir, output_dir, working_dir):
         "--report-output-level=subject",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -160,7 +165,7 @@ def test_multises_post1_qsiprep_reportroot(data_dir, output_dir, working_dir):
         "--recon-spec=test_workflow",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -185,7 +190,7 @@ def test_multises_post1_qsiprep_reportsubject(data_dir, output_dir, working_dir)
         "--recon-spec=test_workflow",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -210,7 +215,7 @@ def test_multises_post1_qsiprep_reportsession(data_dir, output_dir, working_dir)
         "--recon-spec=test_workflow",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -234,7 +239,7 @@ def test_multises_pre1_qsiprep_reportroot(data_dir, output_dir, working_dir):
         "--recon-spec=test_workflow",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -259,7 +264,7 @@ def test_multises_pre1_qsiprep_reportsubject(data_dir, output_dir, working_dir):
         "--recon-spec=test_workflow",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -284,7 +289,7 @@ def test_multises_pre1_qsiprep_reportsession(data_dir, output_dir, working_dir):
         "--recon-spec=test_workflow",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -323,7 +328,7 @@ def test_amico_noddi(data_dir, output_dir, working_dir):
         "--report-output-level=session",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -362,7 +367,7 @@ def test_autotrack(data_dir, output_dir, working_dir):
         "--recon-spec=dsi_studio_autotrack",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -404,7 +409,7 @@ def test_dipy_mapmri(data_dir, output_dir, working_dir):
         "--output-resolution=5",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -445,7 +450,7 @@ def test_dipy_dki(data_dir, output_dir, working_dir):
         "--recon-spec=dipy_dki",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -478,7 +483,7 @@ def test_scalar_mapper(data_dir, output_dir, working_dir):
         "--nthreads=1",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -512,7 +517,7 @@ def test_pyafq_recon_external_trk(data_dir, output_dir, working_dir):
         "--recon-spec=mrtrix_multishell_msmt_pyafq_tractometry",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -546,7 +551,7 @@ def test_pyafq_recon_full(data_dir, output_dir, working_dir):
         "--recon-spec=pyafq_tractometry",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -586,7 +591,7 @@ def test_mrtrix3_recon(data_dir, output_dir, working_dir):
         "4S156Parcels",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
 @pytest.mark.integration
@@ -617,10 +622,10 @@ def test_tortoise_recon(data_dir, output_dir, working_dir):
         "--recon-spec=TORTOISE",
     ]
 
-    _run_and_generate(TEST_NAME, parameters, test_main=True)
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
 
 
-def _run_and_generate(test_name, parameters, test_main=True):
+def _run_and_generate(test_name, parameters, test_main=False):
     from qsirecon import config
 
     # TODO: Add --clean-workdir param to CLI
@@ -637,25 +642,75 @@ def _run_and_generate(test_name, parameters, test_main=True):
 
             assert e.value.code == 0
     else:
-        # XXX: This isn't working because config.execution.fs_license_file is None.
         parse_args(parameters)
         config_file = config.execution.work_dir / f"config-{config.execution.run_uuid}.toml"
         config.loggers.cli.warning(f"Saving config file to {config_file}")
+        config.execution.fs_license_file = freesurfer_license(config.execution.work_dir)
         config.to_filename(config_file)
 
         retval = build_workflow(config_file, retval={})
         qsirecon_wf = retval["workflow"]
-        qsirecon_wf.run()
-        write_derivative_description(config.execution.fmri_dir, config.execution.output_dir)
-
         build_boilerplate(str(config_file), qsirecon_wf)
-        generate_reports(
-            output_level=config.execution.report_output_level,
-            output_dir=config.execution.output_dir,
-            run_uuid=config.execution.run_uuid,
-            qsirecon_suffix="",
+        config.loggers.workflow.log(
+            15,
+            "\n".join(["config:"] + ["\t\t%s" % s for s in config.dumps().splitlines()]),
+        )
+
+        qsirecon_wf.run(**config.nipype.get_plugin())
+
+        write_derivative_description(
+            config.execution.bids_dir,
+            config.execution.output_dir,
+            atlases=config.execution.atlases,
+            dataset_links=config.execution.dataset_links,
         )
 
+        if config.execution.atlases:
+            write_atlas_dataset_description(config.execution.output_dir / "atlases")
+
+        # Compile list of output folders
+        qsirecon_suffixes = config.workflow.qsirecon_suffixes
+        config.loggers.cli.info(f"QSIRecon pipeline suffixes: {qsirecon_suffixes}")
+        failed_reports = []
+        for qsirecon_suffix in qsirecon_suffixes:
+            suffix_dir = str(
+                config.execution.output_dir / "derivatives" / f"qsirecon-{qsirecon_suffix}"
+            )
+
+            # Add other pipeline-specific suffixes to the dataset links
+            other_suffixes = [s for s in qsirecon_suffixes if s != qsirecon_suffix]
+            dataset_links = config.execution.dataset_links.copy()
+            dataset_links["qsirecon"] = str(config.execution.output_dir)
+            dataset_links.update(
+                {
+                    f"qsirecon-{s}": str(
+                        config.execution.output_dir / "derivatives" / f"qsirecon-{s}"
+                    )
+                    for s in other_suffixes
+                }
+            )
+
+            # Copy the boilerplate files
+            copy_boilerplate(config.execution.output_dir, suffix_dir)
+
+            suffix_failed_reports = generate_reports(
+                output_level=config.execution.report_output_level,
+                output_dir=suffix_dir,
+                run_uuid=config.execution.run_uuid,
+                qsirecon_suffix=qsirecon_suffix,
+            )
+            failed_reports += suffix_failed_reports
+            write_derivative_description(
+                config.execution.bids_dir,
+                suffix_dir,
+                atlases=config.execution.atlases,
+                dataset_links=dataset_links,
+            )
+            write_bidsignore(suffix_dir)
+
+        if failed_reports:
+            print(failed_reports)
+
     output_list_file = os.path.join(get_test_data_path(), f"{test_name}_outputs.txt")
     optional_outputs_list = os.path.join(get_test_data_path(), f"{test_name}_optional_outputs.txt")
     if not os.path.isfile(optional_outputs_list):