From c7b10134969d5116d47a9156c9b911db737b26d2 Mon Sep 17 00:00:00 2001
From: Takanori Nakane <nakane.t@gmail.com>
Date: Tue, 20 Aug 2024 13:39:19 +0900
Subject: [PATCH 1/4] FullCBFWriter: repair the panel shuffling bug (#745)

---
 src/dxtbx/format/cbf_writer.py | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/dxtbx/format/cbf_writer.py b/src/dxtbx/format/cbf_writer.py
index 595538ecd..62d72125f 100644
--- a/src/dxtbx/format/cbf_writer.py
+++ b/src/dxtbx/format/cbf_writer.py
@@ -215,6 +215,7 @@ def level_string(key):
         detector_axes_names = []  # save these for later
         panelkeys = []
         panelnames = []
+        panelindices = []
 
         def recursive_setup_basis_dict(key, parent_name="", panel_id=0):
             # Set up CBF axis names, including equipment components and depends_on chains
@@ -230,6 +231,8 @@ def recursive_setup_basis_dict(key, parent_name="", panel_id=0):
                 panelname = "PANEL_%d" % panel_id
                 panelkeys.append(key)
                 panelnames.append(panelname)
+                dxtbx_panel_index = list(detector).index(node)
+                panelindices.append(dxtbx_panel_index)
                 panel_id += 1
 
             if len(key) == 1:
@@ -253,6 +256,11 @@ def recursive_setup_basis_dict(key, parent_name="", panel_id=0):
             return panel_id
 
         recursive_setup_basis_dict((0,))
+        # The order `recursive_setup_basis_dict` visits panels does not necessarily match
+        # the order returned by dxtbx's `get_detector` and `get_raw_data`.
+        # See https://github.com/cctbx/dxtbx/issues/745.
+        self.panelindices = panelindices  # needed in add_data_to_cbf
+        sorted_panels = [detector[i] for i in panelindices]
 
         if index is None:
             cbf_root = self.imageset.paths()[0]
@@ -327,7 +335,7 @@ def recursive_setup_basis_dict(key, parent_name="", panel_id=0):
             # defined as [min-trusted-value, max-trusted-value]. The CBF definition
             # of 'overload' is in fact saturation - i.e. the max-trusted-value, while
             # the undefined_value is below the min-trusted-value.
-            trusted_ranges = [panel.get_trusted_range() for panel in detector]
+            trusted_ranges = [panel.get_trusted_range() for panel in sorted_panels]
             try:
                 add_frame_specific_cbf_tables(
                     cbf,
@@ -336,7 +344,7 @@ def recursive_setup_basis_dict(key, parent_name="", panel_id=0):
                     trusted_ranges,
                     diffrn_id,
                     False,
-                    gain=[panel.get_gain() for panel in detector],
+                    gain=[panel.get_gain() for panel in sorted_panels],
                     flux=beam.get_flux(),
                 )
             except TypeError:
@@ -348,7 +356,7 @@ def recursive_setup_basis_dict(key, parent_name="", panel_id=0):
                     trusted_ranges,
                     diffrn_id,
                     False,
-                    gain=[panel.get_gain() for panel in detector],
+                    gain=[panel.get_gain() for panel in sorted_panels],
                 )
 
         """Data items in the AXIS category record the information required
@@ -596,6 +604,7 @@ def add_data_to_cbf(self, cbf, index=None, data=None, verbose=False):
                 data = self.imageset.get_raw_data(index)
         if not isinstance(data, tuple):
             data = (data,)
+        data = tuple([data[i] for i in self.panelindices])
 
         array_names = []
         cbf.find_category(b"diffrn_data_frame")

From 5d5397b6634ce062cf0fc119d1a1912d7c8b9d6a Mon Sep 17 00:00:00 2001
From: Takanori Nakane <nakane.t@gmail.com>
Date: Tue, 20 Aug 2024 14:00:06 +0900
Subject: [PATCH 2/4] Add newsfragment

---
 newsfragments/XXX.bugfix | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 newsfragments/XXX.bugfix

diff --git a/newsfragments/XXX.bugfix b/newsfragments/XXX.bugfix
new file mode 100644
index 000000000..6dbd045e7
--- /dev/null
+++ b/newsfragments/XXX.bugfix
@@ -0,0 +1 @@
++ repair the panel shuffling bug in FullCBFWriter

From 5354de1e35b54329ce185d5d2bcd0483b7bca26e Mon Sep 17 00:00:00 2001
From: DiamondLightSource-build-server
 <DiamondLightSource-build-server@users.noreply.github.com>
Date: Tue, 20 Aug 2024 12:41:04 +0000
Subject: [PATCH 3/4] Rename newsfragments/XXX.bugfix to
 newsfragments/752.bugfix

---
 newsfragments/{XXX.bugfix => 752.bugfix} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename newsfragments/{XXX.bugfix => 752.bugfix} (100%)

diff --git a/newsfragments/XXX.bugfix b/newsfragments/752.bugfix
similarity index 100%
rename from newsfragments/XXX.bugfix
rename to newsfragments/752.bugfix

From 6d7d15d8d41fe1b642d40d485c32cafea100bea8 Mon Sep 17 00:00:00 2001
From: Nicholas Devenish <ndevenish@gmail.com>
Date: Wed, 21 Aug 2024 09:10:57 +0100
Subject: [PATCH 4/4] Reword news

---
 newsfragments/752.bugfix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/newsfragments/752.bugfix b/newsfragments/752.bugfix
index 6dbd045e7..f01107525 100644
--- a/newsfragments/752.bugfix
+++ b/newsfragments/752.bugfix
@@ -1 +1 @@
-+ repair the panel shuffling bug in FullCBFWriter
+Stop ``dxtbx.image_average`` shuffling panel positions for segmented detectors.