From 87850ec84d2e14e01f63499053865f0bf30ea47b Mon Sep 17 00:00:00 2001
From: Victor Perez Meza <victor.x.perezmesa@gsk.com>
Date: Mon, 4 Nov 2024 11:22:39 +0100
Subject: [PATCH] added illumination correction with basicpy

---
 macsima2mc/CLI.py        |  6 ++++++
 macsima2mc/macsima2mc.py | 11 +++++++++--
 macsima2mc/tools.py      |  4 ++--
 3 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/macsima2mc/CLI.py b/macsima2mc/CLI.py
index 46ed35f..a6b3ea9 100644
--- a/macsima2mc/CLI.py
+++ b/macsima2mc/CLI.py
@@ -29,6 +29,12 @@ def get_args():
                     help='string specifying the name of the reference marker'
                     )
 
+    parser.add_argument('-od',
+                    '--output_dir',
+                    default='raw',
+                    help='string specifying the name of the reference marker'
+                    )
+
     parser.add_argument('-ic',
                     '--illumination_correction',
                     action='store_true',
diff --git a/macsima2mc/macsima2mc.py b/macsima2mc/macsima2mc.py
index 4cf70a8..084be09 100644
--- a/macsima2mc/macsima2mc.py
+++ b/macsima2mc/macsima2mc.py
@@ -12,11 +12,18 @@ def main(args):
     input=args.input
     output=args.output
     ref=args.reference_marker
-    basicpy_corr=args.illumination_correction 
+    basicpy_corr=args.illumination_correction
+    out_folder_name=args.output_dir
+
     cycle_info=tools.cycle_info( input , macsima_pattern(version=2),ref_marker= ref)
     cycle_info=tools.append_metadata( cycle_info )
     #cycle_info.to_csv( args.output / 'cycle_{c}_info.csv'.format(c=f'{6:03d}'), index=False )
-    output_dirs=tools.create_stack( cycle_info, output ,ref_marker=ref,hi_exp=args.hi_exposure_only,ill_corr=basicpy_corr)
+    output_dirs=tools.create_stack( cycle_info, output ,
+                                    ref_marker=ref,
+                                    hi_exp=args.hi_exposure_only,
+                                    ill_corr=basicpy_corr,
+                                    out_folder=out_folder_name
+                                    )
     [mc_tools.write_markers_file(path)  for path in output_dirs]
         
 
diff --git a/macsima2mc/tools.py b/macsima2mc/tools.py
index a534fa2..dc48e1c 100644
--- a/macsima2mc/tools.py
+++ b/macsima2mc/tools.py
@@ -184,7 +184,7 @@ def select_by_exposure(list_indices,exp_index=4,target='max'):
 
     return selected_indices
 
-def create_stack(cycle_info_df,output_dir,ref_marker='DAPI',hi_exp=False,ill_corr=False,extended_outputs=False):
+def create_stack(cycle_info_df,output_dir,ref_marker='DAPI',hi_exp=False,ill_corr=False,out_folder='raw',extended_outputs=False):
 
     if extended_outputs:
         out=outputs_dic()
@@ -198,7 +198,7 @@ def create_stack(cycle_info_df,output_dir,ref_marker='DAPI',hi_exp=False,ill_cor
         acq_index=select_by_exposure(acq_index)
 
     for index in acq_index:
-        stack_output_dir=output_dir / cast_outdir_name(index) / 'staged'
+        stack_output_dir=output_dir / cast_outdir_name(index) / out_folder
         ( stack_output_dir ).mkdir(parents=True, exist_ok=True)
         group=acq_group.get_group(index)
         #use tile 1 as reference to determine the heigh and width of the tiles