From e030265c8540cd6669860ee9458df3a027b4f633 Mon Sep 17 00:00:00 2001
From: Lorenzo Gaifas <brisvag@gmail.com>
Date: Fri, 26 Apr 2024 16:53:29 +0200
Subject: [PATCH] add dose, better logging

---
 src/waretomo/_parse.py | 13 +++++++++++--
 src/waretomo/main.py   | 30 ++++++++++++++++++++++++++++--
 2 files changed, 39 insertions(+), 4 deletions(-)

diff --git a/src/waretomo/_parse.py b/src/waretomo/_parse.py
index 9492909..bc116e2 100644
--- a/src/waretomo/_parse.py
+++ b/src/waretomo/_parse.py
@@ -6,7 +6,15 @@
 
 
 def parse_data(
-    progress, warp_dir, mdoc_dir, output_dir, roi_dir, just=(), exclude=(), train=False
+    progress,
+    warp_dir,
+    mdoc_dir,
+    output_dir,
+    roi_dir,
+    just=(),
+    exclude=(),
+    train=False,
+    dose=None,
 ):
     log = logging.getLogger("waretomo")
 
@@ -34,6 +42,7 @@ def parse_data(
     tilt_series_unprocessed = []
 
     for mdoc_file in progress.track(mdocs, description="Reading mdocs..."):
+        log.info(f"Parsing {mdoc_file}.")
         mdoc = Mdoc.from_file(mdoc_file)
 
         # warp uses mdoc name in many places, but some times the ts_name is important
@@ -110,7 +119,7 @@ def parse_data(
         else:
             roi_file = None
 
-        dose = mdoc.section_data[0].ExposureDose
+        dose = mdoc.section_data[0].ExposureDose if dose is None else dose
         if not dose:
             log.error("Exposure dose not present in mdoc! Setting to 0.")
         px_size_raw = mdoc.section_data[0].PixelSpacing
diff --git a/src/waretomo/main.py b/src/waretomo/main.py
index 3e5b867..e6f97de 100644
--- a/src/waretomo/main.py
+++ b/src/waretomo/main.py
@@ -46,7 +46,12 @@ def __str__(self):
     is_flag=True,
     help="only print some info, without running the commands.",
 )
-@click.option("-v", "--verbose", count=True, help="echo all individual commands")
+@click.option(
+    "-v",
+    "--verbose",
+    count=True,
+    help="level of verbosity; can be passed multiple times.",
+)
 @click.option(
     "-j",
     "--just",
@@ -82,6 +87,11 @@ def __str__(self):
     default=4,
     help="binning for aretomo reconstruction (relative to warp pre-processed binning)",
 )
+@click.option(
+    "--dose",
+    type=float,
+    help="exposure dose (e/A^2/tilt_image). If not passed, guess from mdocs.",
+)
 @click.option(
     "-a", "--tilt-axis", type=float, help="starting tilt axis for AreTomo, if any"
 )
@@ -159,6 +169,7 @@ def cli(
     sample_thickness,
     z_thickness,
     binning,
+    dose,
     tilt_axis,
     patches,
     roi_dir,
@@ -246,6 +257,7 @@ def cli(
             just=just,
             exclude=exclude,
             train=train,
+            dose=dose,
         )
 
         aretomo_kwargs = {
@@ -321,7 +333,21 @@ def cli(
         ts = tilt_series[0]
         ts_name = ts["name"]
         ts_info = {k: v for k, v in ts.items() if k not in ("even", "odd")}
-        log.info(f'Metadata from tiltseries "{ts_name}": {ts_info}')
+        ts_info = {
+            k: (str(v.relative_to(warp_dir)) if isinstance(v, Path) else v)
+            for k, v in ts_info.items()
+            if k
+        }
+        ts_info.update(ts_info.pop("aretomo_kwargs"))
+        ts_info = "".join(f'{nl}{" " * 12}- {k}: {v}' for k, v in ts_info.items())
+        first_ts_summary = cleandoc(
+            f"""
+            Double check that these values make sense for {ts_name}:
+            {ts_info}
+            """
+        )
+
+        print(Panel(first_ts_summary))
 
         if not dry_run:
             with open(output_dir / "waretomo.log", "a") as f: