From b3f5dfcc8be3afdc17aca7d43c93474e585ecaa3 Mon Sep 17 00:00:00 2001
From: Chris Allan <callan@glencoesoftware.com>
Date: Tue, 29 Jun 2021 12:13:57 +0100
Subject: [PATCH] Bring implementation in line with comments

---
 isyntax2raw/__init__.py        | 22 ++++++++++------------
 isyntax2raw/cli/isyntax2raw.py |  4 ++--
 2 files changed, 12 insertions(+), 14 deletions(-)

diff --git a/isyntax2raw/__init__.py b/isyntax2raw/__init__.py
index f78f15e..353a1d8 100644
--- a/isyntax2raw/__init__.py
+++ b/isyntax2raw/__init__.py
@@ -375,13 +375,10 @@ def wait_any(self, regions):
         else:
             return self.pixel_engine.wait_any(regions)
 
-    def write_metadata_json_cli(self):
-        self.write_metadata_json(self.slide_directory)
-
-    def write_metadata_json(self, output_file_path):
+    def write_metadata_json(self, metadata_file):
         '''write metadata to a JSON file'''
 
-        with open(output_file_path, "w", encoding="utf-8") as f:
+        with open(metadata_file, "w", encoding="utf-8") as f:
             metadata = self.get_metadata()
 
             for image in range(self.num_images()):
@@ -390,7 +387,7 @@ def write_metadata_json(self, output_file_path):
 
             json.dump(metadata, f)
 
-    def write_metadata_xml(self):
+    def write_metadata_xml(self, metadata_file):
         ome_timestamp = self.acquisition_datetime()
 
         xml_values = {
@@ -421,20 +418,21 @@ def write_metadata_xml(self):
         loader = PackageLoader()
         template = loader.import_("isyntax2raw.resources.ome_template")
         xml = template(xml_values).render()
-        ome_xml_file = os.path.join(
-            self.slide_directory, "OME", "METADATA.ome.xml"
-        )
-        with open(ome_xml_file, "w", encoding="utf-8") as omexml:
+        with open(metadata_file, "w", encoding="utf-8") as omexml:
             omexml.write(xml)
 
     def write_metadata(self):
         os.makedirs(os.path.join(self.slide_directory, "OME"), exist_ok=True)
+
         metadata_file = os.path.join(
             self.slide_directory, "OME", "METADATA.json"
         )
-
         self.write_metadata_json(metadata_file)
-        self.write_metadata_xml()
+
+        metadata_file = os.path.join(
+            self.slide_directory, "OME", "METADATA.ome.xml"
+        )
+        self.write_metadata_xml(metadata_file)
 
     def get_size(self, dim_range):
         '''calculate the length in pixels of a dimension'''
diff --git a/isyntax2raw/cli/isyntax2raw.py b/isyntax2raw/cli/isyntax2raw.py
index 8bec27b..e131efd 100644
--- a/isyntax2raw/cli/isyntax2raw.py
+++ b/isyntax2raw/cli/isyntax2raw.py
@@ -87,9 +87,9 @@ def write_tiles(
 def write_metadata(debug, input_path, output_file):
     with WriteTiles(
         None, None, None, None,
-        None, None, None, input_path, output_file
+        None, None, None, input_path, None
     ) as wt:
-        wt.write_metadata_json_cli()
+        wt.write_metadata_json(output_file)
 
 
 def main():