From aebb3d9e16ed8e6f48c2661f1594874008112ff6 Mon Sep 17 00:00:00 2001
From: David McDonagh <60879630+toastisme@users.noreply.github.com>
Date: Mon, 12 Aug 2024 08:41:29 +0100
Subject: [PATCH 1/3] Additional methods for FormatISISSXD to extract data more
 efficiently. (#743)

---
 newsfragments/743.misc            |  1 +
 src/dxtbx/format/FormatISISSXD.py | 95 +++++++++++++++++++++++++++----
 2 files changed, 86 insertions(+), 10 deletions(-)
 create mode 100644 newsfragments/743.misc

diff --git a/newsfragments/743.misc b/newsfragments/743.misc
new file mode 100644
index 000000000..5574bbb6f
--- /dev/null
+++ b/newsfragments/743.misc
@@ -0,0 +1 @@
+Additional methods for FormatISISSXD to extract data more efficiently.
diff --git a/src/dxtbx/format/FormatISISSXD.py b/src/dxtbx/format/FormatISISSXD.py
index 00299d515..549fe3064 100644
--- a/src/dxtbx/format/FormatISISSXD.py
+++ b/src/dxtbx/format/FormatISISSXD.py
@@ -3,6 +3,7 @@
 from typing import List, Tuple
 
 import h5py
+import numpy as np
 
 import cctbx.array_family.flex as flex
 
@@ -44,6 +45,9 @@ def get_name(image_file: str) -> str:
 
         return get_name(image_file) == "SXD"
 
+    def get_instrument_name(self) -> str:
+        return "SXD"
+
     def get_experiment_title(self) -> str:
         return self._nxs_file["raw_data_1"]["title"][0].decode()
 
@@ -55,23 +59,26 @@ def get_experiment_description(self) -> str:
         run_number = self.get_experiment_run_number()
         return f"{title} ({run_number})"
 
-    def get_goniometer(self, idx: int = None) -> Goniometer:
-        rotation_axis = (0.0, 1.0, 0.0)
-        fixed_rotation = (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0)
-        goniometer = GoniometerFactory.make_goniometer(rotation_axis, fixed_rotation)
+    def get_goniometer_phi_angle(self) -> float:
         try:
             experiment_title = self.get_experiment_title()
             if "w=" in experiment_title:
-                angle = float(experiment_title().split("w=")[1].split()[0])
+                return float(experiment_title.split("w=")[1].split()[0])
             elif "wccr" in experiment_title:
-                angle = float(experiment_title.split("wccr=")[1].split()[0])
+                return float(experiment_title.split("wccr=")[1].split()[0])
             elif "wtl" in experiment_title:
-                angle = float(experiment_title.split("wtl=")[1].split()[0])
+                return float(experiment_title.split("wtl=")[1].split()[0])
             else:
-                return goniometer
-            goniometer.rotate_around_origin(rotation_axis, angle)
+                return 0
         except (ValueError, IndexError):
-            pass
+            return 0
+
+    def get_goniometer(self, idx: int = None) -> Goniometer:
+        rotation_axis = (0.0, 1.0, 0.0)
+        fixed_rotation = (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0)
+        goniometer = GoniometerFactory.make_goniometer(rotation_axis, fixed_rotation)
+        angle = self.get_goniometer_phi_angle()
+        goniometer.rotate_around_origin(rotation_axis, angle)
         return goniometer
 
     def get_detector(self, index: int = None) -> Detector:
@@ -313,3 +320,71 @@ def get_raw_data(self, index: int, use_loaded_data=True) -> Tuple[flex.int]:
                 raw_data.append(panel_data)
 
         return tuple(raw_data)
+
+    def get_flattened_data(
+        self, image_range: None | Tuple = None, scale_data: bool = True
+    ) -> Tuple[flex.int]:
+        """
+        Image data summed along the time-of-flight direction
+        """
+
+        panel_size = self._get_image_size()
+        total_pixels = panel_size[0] * panel_size[1]
+        # Panel positions are offset by 4 in raw_data array
+        # See p24 of https://www.isis.stfc.ac.uk/Pages/sxd-user-guide6683.pdf
+        idx_offset = 4
+        max_val = None
+        num_tof_bins = len(self._get_time_of_flight())
+        raw_data = []
+        for panel_idx in range(self._get_num_panels()):
+            start_idx = (panel_idx * total_pixels) + (panel_idx * idx_offset)
+            end_idx = start_idx + total_pixels
+            panel_data = self._nxs_file["raw_data_1/detector_1/counts"][
+                0, start_idx:end_idx, :
+            ]
+            panel_data = np.reshape(
+                panel_data, (panel_size[0], panel_size[1], num_tof_bins)
+            )
+            if image_range is not None:
+                assert (
+                    len(image_range) == 2
+                ), "expected image_range to be only two values"
+                assert (
+                    image_range[0] >= 0 and image_range[0] < image_range[1]
+                ), "image_range[0] out of range"
+                assert image_range[1] <= num_tof_bins, "image_range[1] out of range"
+                panel_data = np.flipud(
+                    np.sum(panel_data[:, :, image_range[0] : image_range[1]], axis=2)
+                )
+            else:
+                panel_data = np.flipud(np.sum(panel_data, axis=2))
+            if panel_idx == 0 and self._panel_0_flipped():
+                panel_data = np.flipud(panel_data)
+            panel_max_val = np.max(panel_data)
+            if max_val is None or max_val < panel_max_val:
+                max_val = panel_max_val
+            raw_data.append(panel_data)
+
+        if scale_data:
+            return tuple([(i / max_val).tolist() for i in raw_data])
+
+        return tuple([i.tolist() for i in raw_data])
+
+    def get_flattened_pixel_data(
+        self, panel_idx: int, x: int, y: int
+    ) -> Tuple[Tuple, Tuple]:
+        time_channels = self._get_time_of_flight()
+        panel_size = self._get_image_size()
+        height = panel_size[1]
+        total_pixels = panel_size[0] * panel_size[1]
+        # Panel positions are offset by 4 in raw_data array
+        # See p24 of https://www.isis.stfc.ac.uk/Pages/sxd-user-guide6683.pdf
+        idx_offset = 4
+        idx = (panel_idx * total_pixels) + (panel_idx * idx_offset) + y * height + x
+        return (
+            time_channels,
+            tuple(self._nxs_file["raw_data_1/detector_1/counts"][0, idx, :].tolist()),
+        )
+
+    def get_proton_charge(self):
+        return float(self._nxs_file["raw_data_1/proton_charge"][0])

From f3635adf57634bffefff7ecb628a889dec1468b6 Mon Sep 17 00:00:00 2001
From: Nicholas Devenish <ndevenish@gmail.com>
Date: Fri, 16 Aug 2024 13:16:01 +0100
Subject: [PATCH 2/3] Pin numpy to <2 for CI (#750)

We will need to address this at some point soon, but for now just fix the CI.
---
 .azure-pipelines/ci-conda-env.txt | 6 +++---
 newsfragments/750.misc            | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)
 create mode 100644 newsfragments/750.misc

diff --git a/.azure-pipelines/ci-conda-env.txt b/.azure-pipelines/ci-conda-env.txt
index d9c93bc90..23081b8ff 100644
--- a/.azure-pipelines/ci-conda-env.txt
+++ b/.azure-pipelines/ci-conda-env.txt
@@ -1,10 +1,10 @@
 conda-forge::boost
 conda-forge::boost-cpp
 conda-forge::bzip2
-conda-forge::c-compiler<1.5
+conda-forge::c-compiler
 conda-forge::cctbx-base
 conda-forge::conda
-conda-forge::cxx-compiler<1.5
+conda-forge::cxx-compiler
 conda-forge::python-dateutil
 conda-forge::dials-data
 conda-forge::docutils
@@ -16,7 +16,7 @@ conda-forge::hdf5
 conda-forge::matplotlib-base
 conda-forge::mrcfile
 conda-forge::natsort
-conda-forge::numpy
+conda-forge::numpy<2
 conda-forge::nxmx
 conda-forge::orderedset
 conda-forge::pillow>=5.4.1
diff --git a/newsfragments/750.misc b/newsfragments/750.misc
new file mode 100644
index 000000000..af2ac0bf2
--- /dev/null
+++ b/newsfragments/750.misc
@@ -0,0 +1 @@
+Fix CI by pinning numpy 2.0.

From 9a8cff3d26488948b6bc0f468e3f0bf1e611bfd5 Mon Sep 17 00:00:00 2001
From: Nicholas Devenish <ndevenish@gmail.com>
Date: Fri, 16 Aug 2024 13:38:40 +0100
Subject: [PATCH 3/3] Maintenance: Set a CMake policy version (#749)

3.30 added a new policy around pending removal of the FindBoost module. This
is quite noisy without this setting.
---
 CMakeLists.txt         | 2 +-
 newsfragments/749.misc | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)
 create mode 100644 newsfragments/749.misc

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 96c6b76d5..c356a050e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.20 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.20...3.30 FATAL_ERROR)
 
 project(dxtbx LANGUAGES C CXX)
 
diff --git a/newsfragments/749.misc b/newsfragments/749.misc
new file mode 100644
index 000000000..a18f8bf2a
--- /dev/null
+++ b/newsfragments/749.misc
@@ -0,0 +1 @@
+Set a CMake policy version, to avoid warnings on newer version.