fix topaz stuff!

pyproject.toml

@@ -28,11 +28,11 @@ dynamic = ["version"]
 dependencies = [
     "GPUtil",
     "click",
-    "mdocfile",
+    "mdocfile==0.1.0",
     "pandas",
     "rich",
-    "topaz-em",
     "sh",
+    "topaz-em==0.2.5",
 ]
 
 # extras

src/waretomo/_topaz.py

@@ -12,18 +12,22 @@
 
 def _run_and_update_progress(progress, task, func, *args, **kwargs):
     std = io.StringIO()
+
+    def _run_with_redirection():
+        with contextlib.redirect_stderr(std):
+            func(*args, **kwargs)
+
     with futures.ThreadPoolExecutor(1) as executor:
-        with contextlib.redirect_stderr(std), contextlib.redirect_stdout(std):
-            job = executor.submit(func, *args, **kwargs)
+        job = executor.submit(_run_with_redirection)
 
-            last_read_pos = 0
-            while not job.done():
-                time.sleep(0.5)
-                std.seek(last_read_pos)
-                last = std.read()
-                if match := re.search(r"(\d+\.\d+)%", last):
-                    last_read_pos = std.tell()
-                    progress.update(task, completed=float(match.group(1)))
+        last_read_pos = 0
+        while not job.done():
+            time.sleep(0.5)
+            std.seek(last_read_pos)
+            last = std.read()
+            if match := re.search(r"(\d+\.\d+)%", last):
+                last_read_pos = std.tell()
+                progress.update(task, completed=float(match.group(1)), refresh=True)
 
         try:
             return job.result()
@@ -46,41 +50,49 @@ def topaz_batch(
     train=False,
     tile_size=32,
     patch_size=32,
+    gpus=None,
     dry_run=False,
     verbose=False,
     overwrite=False,
 ):
-    set_num_threads(0)
-    if train:
-        task = progress.add_task(description="Training...")
-        model, _ = _run_and_update_progress(
-            progress,
-            task,
-            train_model,
-            even_path=even,
-            odd_path=odd,
-            save_prefix=str(outdir / "trained_models" / model_name),
-            save_interval=10,
-            device=-2,
-            tilesize=patch_size,
-            base_kernel_width=11,
-            num_workers=multiprocessing.cpu_count(),
-        )
-    else:
-        model = load_model(model_name, base_kernel_width=11)
-    model.eval()
-    model, use_cuda, num_devices = set_device(model, -2)
-
     inputs = [ts["recon"] for ts in tilt_series]
 
     if verbose:
+        if train:
+            print(f"training model: '{model_name}' with inputs '{even}' and '{odd}'")
         if len(inputs) > 2:
             print(f"denoising: [{inputs[0]} [...] {inputs[-1]}]")
         else:
             print(f"denoising: {inputs}")
         print(f"output: {outdir}")
 
     if not dry_run:
+        set_num_threads(0)
+        std = io.StringIO()
+        if train:
+            task = progress.add_task(description="Training...")
+            model, _ = _run_and_update_progress(
+                progress,
+                task,
+                train_model,
+                even_path=even,
+                odd_path=odd,
+                save_prefix=str(outdir / "trained_models" / model_name),
+                save_interval=10,
+                device=-2
+                if gpus is None
+                else next(iter(gpus)),  # TODO: actually run with multiple gpus?
+                tilesize=patch_size,
+                base_kernel_width=11,
+                num_workers=multiprocessing.cpu_count(),
+            )
+        else:
+            with contextlib.redirect_stdout(std):
+                model = load_model(model_name, base_kernel_width=11)
+        with contextlib.redirect_stdout(std):
+            model.eval()
+            model, use_cuda, num_devices = set_device(model, -2)
+
         for path in progress.track(inputs, description="Denoising..."):
             subtask = progress.add_task(description=path.name)
             _run_and_update_progress(

src/waretomo/main.py

@@ -255,9 +255,10 @@ def cli(
             "verbose": verbose,
         }
 
-        topaz_opts = {
+        topaz_kwargs = {
             "train": train,
             "model_name": topaz_model,
+            "gpus": gpus,
             "tile_size": topaz_tile_size,
             "patch_size": topaz_patch_size,
         }
@@ -289,7 +290,9 @@ def cli(
         aretomo_opts_log = "".join(
             f'{nl}{" " * 12}- {k}: {v}' for k, v in aretomo_kwargs.items()
         )
-        topaz_log = "".join(f'{nl}{" " * 12}- {k}: {v}' for k, v in topaz_opts.items())
+        topaz_log = "".join(
+            f'{nl}{" " * 12}- {k}: {v}' for k, v in topaz_kwargs.items()
+        )
 
         print(
             Panel(
@@ -402,6 +405,6 @@ def cli(
                 outdir=outdir_denoised,
                 even=str(output_dir / "even"),
                 odd=str(output_dir / "odd"),
-                **topaz_opts,
+                **topaz_kwargs,
                 **meta_kwargs,
             )