From 41d7f6bca832f657417dc93f0c1ab2c8a0afcc4b Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Tue, 26 Apr 2022 08:42:28 +0200
Subject: [PATCH] enh: incorporate new custom plugin

---
 mriqc/cli/run.py       | 18 +++++++++++++-----
 mriqc/config.py        |  8 ++++++++
 mriqc/engine/plugin.py |  4 ++--
 3 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/mriqc/cli/run.py b/mriqc/cli/run.py
index 6d8cef8ed..7c46aa69c 100644
--- a/mriqc/cli/run.py
+++ b/mriqc/cli/run.py
@@ -52,21 +52,23 @@ def main():
 
     # Set up participant level
     if "participant" in config.workflow.analysis_level:
-        _plugin = config.nipype.get_plugin()
+        _pool = None
         if config.nipype.plugin in ("MultiProc", "LegacyMultiProc"):
             from contextlib import suppress
             import multiprocessing as mp
             import multiprocessing.forkserver
-            from mriqc.engine.plugin import MultiProcPlugin
+            from concurrent.futures import ProcessPoolExecutor
 
             with suppress(RuntimeError):
                 mp.set_start_method("forkserver")
                 mp.forkserver.ensure_running()
             gc.collect()
 
-            _plugin = {
-                "plugin": MultiProcPlugin(plugin_args=config.nipype.plugin_args),
-            }
+            _pool = ProcessPoolExecutor(
+                max_workers=config.nipype.nprocs,
+                initializer=config._process_initializer,
+                initargs=(config.execution.cwd,),
+            )
 
         _resmon = None
         if config.execution.resource_monitor:
@@ -138,6 +140,12 @@ def main():
             # Clean up master process before running workflow, which may create forks
             gc.collect()
             # run MRIQC
+            _plugin = config.nipype.get_plugin()
+            if _pool:
+                from mriqc.engine.plugin import MultiProcPlugin
+                _plugin = {
+                    "plugin": MultiProcPlugin(pool=_pool, plugin_args=config.nipype.plugin_args),
+                }
             mriqc_wf.run(**_plugin)
 
             # Warn about submitting measures AFTER
diff --git a/mriqc/config.py b/mriqc/config.py
index 0a0d2deac..38af2ccc0 100644
--- a/mriqc/config.py
+++ b/mriqc/config.py
@@ -346,6 +346,8 @@ class execution(_Config):
     """Path to the directory containing SQLite database indices for the input BIDS dataset."""
     bids_description_hash = None
     """Checksum (SHA256) of the ``dataset_description.json`` of the BIDS dataset."""
+    cwd = os.getcwd()
+    """Current working directory."""
     debug = False
     """Run in sloppy mode (meaning, suboptimal parameters that minimize run-time)."""
     dry_run = False
@@ -630,3 +632,9 @@ def to_filename(filename):
     filename = Path(filename)
     filename.parent.mkdir(exist_ok=True, parents=True)
     filename.write_text(dumps())
+
+
+def _process_initializer(cwd):
+    """Initialize the environment of the child process."""
+    os.chdir(cwd)
+    os.environ["NIPYPE_NO_ET"] = "1"
diff --git a/mriqc/engine/plugin.py b/mriqc/engine/plugin.py
index e6295dd36..a812554fa 100644
--- a/mriqc/engine/plugin.py
+++ b/mriqc/engine/plugin.py
@@ -418,7 +418,7 @@ class MultiProcPlugin(DistributedPluginBase):
     - mp_context: name of multiprocessing context to use
     """
 
-    def __init__(self, plugin_args=None):
+    def __init__(self, pool=None, plugin_args=None):
         """Initialize the plugin."""
         from mriqc import config
 
@@ -441,7 +441,7 @@ def __init__(self, plugin_args=None):
 
         # Instantiate different thread pools for non-daemon processes
         mp_context = mp.get_context(self.plugin_args.get("mp_context"))
-        self.pool = ProcessPoolExecutor(
+        self.pool = pool or ProcessPoolExecutor(
             max_workers=self.processors,
             initializer=process_initializer,
             initargs=(self._cwd,),