From 029c926a399b80cecb88d510f35426561e4e6116 Mon Sep 17 00:00:00 2001
From: Agustin Corbat <agustin.corbat@scilifelab.se>
Date: Tue, 23 Jul 2024 16:50:47 +0200
Subject: [PATCH] Add the option to choose alignment channel by name

---
 ashlar/filepattern.py    | 9 ++++++++-
 ashlar/fileseries.py     | 9 ++++++++-
 ashlar/scripts/ashlar.py | 5 +++--
 3 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/ashlar/filepattern.py b/ashlar/filepattern.py
index 6b678153..b56bf02c 100644
--- a/ashlar/filepattern.py
+++ b/ashlar/filepattern.py
@@ -98,6 +98,13 @@ def tile_rc(self, i):
         row = i // self.width + self.row_offset
         col = i % self.width + self.col_offset
         return row, col
+    
+    def get_from_channel_map(self, c):
+        if isinstance(c, int):
+            return self.channel_map[c]
+        if c in list(self.channel_map.values()):
+            return c
+        raise Exception(f"{c} was notrecognized as a channel")
 
 
 class FilePatternReader(reg.Reader):
@@ -119,5 +126,5 @@ def read(self, series, c):
 
     def filename(self, series, c):
         row, col = self.metadata.tile_rc(series)
-        c = self.metadata.channel_map[c]
+        c = self.metadata.get_from_channel_map(c)
         return self.pattern.format(row=row, col=col, channel=c)
diff --git a/ashlar/fileseries.py b/ashlar/fileseries.py
index 876db0e3..a2d166c0 100644
--- a/ashlar/fileseries.py
+++ b/ashlar/fileseries.py
@@ -186,10 +186,17 @@ def tile_rc(self, i):
             if self.layout == "snake" and col % 2 == 1:
                 row = self.height - 1 - row
         return row, col
+    
+    def get_from_channel_map(self, c):
+        if isinstance(c, int):
+            return self.channel_map[c]
+        if c in list(self.channel_map.values()):
+            return c
+        raise Exception(f"{c} was notrecognized as a channel")
 
     def filename(self, series, c):
         well, series = self.all_series[self.active_series[series]]
-        c = self.channel_map[c]
+        c = self.get_from_channel_map(c)
         components = self.filename_components[well, series, c]
         return self.pattern.format(**components)
 
diff --git a/ashlar/scripts/ashlar.py b/ashlar/scripts/ashlar.py
index 663fbac2..faa287bf 100644
--- a/ashlar/scripts/ashlar.py
+++ b/ashlar/scripts/ashlar.py
@@ -33,10 +33,11 @@ def main(argv=sys.argv):
               " exist."),
     )
     parser.add_argument(
-        '-c', '--align-channel', dest='align_channel', type=int,
+        '-c', '--align-channel', dest='align_channel',
         default='0', metavar='CHANNEL',
         help=('Reference channel number for image alignment. Numbering starts'
-              ' at 0.'),
+              ' at 0. If fileseries or filepattern is used, it may be channel'
+              ' name.'),
     )
     parser.add_argument(
         '--flip-x', default=False, action='store_true',