From 309f4ab7976432713d779c3b7249183c2e02c8fd Mon Sep 17 00:00:00 2001
From: Ben Williams <benjaminhwilliams@users.noreply.github.com>
Date: Thu, 24 Nov 2022 21:48:32 +0000
Subject: [PATCH 01/30] Add gated image binning for SSX

Add a command line tool for binning each gated batch of images to a
single image.
---
 src/tristan/command_line/__init__.py |  19 +++++
 src/tristan/command_line/images.py   | 121 +++++++++++++++++++++++++++
 2 files changed, 140 insertions(+)

diff --git a/src/tristan/command_line/__init__.py b/src/tristan/command_line/__init__.py
index 1d67b9d9..5bf90b17 100644
--- a/src/tristan/command_line/__init__.py
+++ b/src/tristan/command_line/__init__.py
@@ -421,3 +421,22 @@ def positive_int(value: SupportsInt) -> int:
 group.add_argument(
     "-x", "--num-sequences", help="Number of image sequences.", type=positive_int
 )
+
+# A parser for specifying a pair of trigger signals with which to gate event processing.
+gate_parser = argparse.ArgumentParser(add_help=False)
+gate_parser.add_argument(
+    "-g",
+    "--gate-open",
+    help="Trigger signal denoting the start of each gate period.",
+    choices=triggers.keys(),
+    required=True,
+)
+gate_parser.add_argument(
+    "-c",
+    "--gate-close",
+    help="Trigger signal denoting the end of each gate period (optional).  If not "
+    "provided, this will default to the complementary signal to the '--gate-open' "
+    "value.  For example, if the '--gate-open' signal is 'TTL-rising', "
+    "the --gate-close signal will default to 'TTL-falling', and vice versa.",
+    choices=triggers.keys(),
+)
diff --git a/src/tristan/command_line/images.py b/src/tristan/command_line/images.py
index 449a1f75..047f814e 100644
--- a/src/tristan/command_line/images.py
+++ b/src/tristan/command_line/images.py
@@ -47,6 +47,7 @@
     check_output_file,
     data_files,
     exposure_parser,
+    gate_parser,
     image_output_parser,
     input_parser,
     interval_parser,
@@ -529,6 +530,116 @@ def multiple_sequences_cli(args):
     print(f"Images written to\n\t{output_nexus_pattern or out_file_pattern}")
 
 
+def gated_images_cli(args):
+    """Utility to bin events into a sequence of images according to a gating signal."""
+    write_mode = "w" if args.force else "x"
+    output_file = check_output_file(args.output_file, args.stem, "images", args.force)
+
+    input_nexus = args.data_dir / f"{args.stem}.nxs"
+    if not input_nexus.exists():
+        print(
+            "Could not find a NeXus file containing experiment metadata.\n"
+            "Resorting to writing raw image data without accompanying metadata."
+        )
+
+    image_size = args.image_size or determine_image_size(input_nexus)
+
+    raw_files, _ = data_files(args.data_dir, args.stem)
+
+    # If gate_close isn't specified, default to the complementary signal to gate_open.
+    gate_open = triggers.get(args.gate_open)
+    gate_close = triggers.get(args.gate_close) or gate_open ^ (1 << 5)
+
+    with latrd_data(raw_files, keys=cue_keys) as cues_data:
+        print("Finding detector shutter open and close times.")
+        with ProgressBar():
+            start, end = find_start_end(cues_data)
+
+        print("Finding gate signal times.")
+        open_times = cue_times(cues_data, gate_open, after=start)
+        close_times = cue_times(cues_data, gate_close, after=start)
+        with ProgressBar():
+            open_times, close_times = dask.compute(open_times, close_times)
+
+    if not open_times.size:
+        sys.exit(f"Could not find a '{cues[gate_open]}' signal.")
+    if not close_times.size:
+        sys.exit(f"Could not find a '{cues[gate_close]}' signal.")
+    if not open_times.size == close_times.size:
+        sys.exit(
+            "Found a non-matching number of gate open and close signals:\n\t"
+            f"Number of '{cues[gate_open]}' signals: {open_times.size}\n\t"
+            f"Number of '{cues[gate_close]}' signals: {close_times.size}\n"
+            f"Note that signals before the shutter open time are ignored."
+        )
+
+    open_times.sort_values(inplace=True)
+    close_times.sort_values(inplace=True)
+
+    num_images = open_times.size
+
+    if input_nexus.exists():
+        try:
+            # Write output NeXus file if we have an input NeXus file.
+            output_nexus = CopyTristanNexus.multiple_images_nexus(
+                output_file,
+                input_nexus,
+                nbins=num_images,
+                write_mode=write_mode,
+            )
+        except FileExistsError:
+            sys.exit(
+                f"This output file already exists:\n\t"
+                f"{output_file.with_suffix('.nxs')}\n"
+                "Use '-f' to override, "
+                "or specify a different output file path with '-o'."
+            )
+    else:
+        output_nexus = None
+
+    print(f"Binning events into {num_images} images.")
+
+    # Make a cache for the images.
+    images = create_cache(output_file, num_images, image_size)
+
+    with latrd_data(raw_files, keys=(event_location_key, event_time_key)) as data:
+        # Consider only those events that occur between the start and end times.
+        data = valid_events(data, start, end)
+
+        # Gate the events.
+        event_times = data[event_time_key].values
+        open_index = da.digitize(event_times, open_times) - 1
+        close_index = da.digitize(event_times, close_times) - 1
+        data["time_bin"] = open_index
+        open_times = da.take(open_times, open_index)
+        close_times = da.take(close_times, close_index)
+        data = valid_events(data, open_times, close_times)
+        data.drop(columns=event_time_key, inplace=True)
+
+        # Convert the event IDs to a form that is suitable for a NumPy bincount.
+        data[event_location_key] = pixel_index(data[event_location_key], image_size)
+
+        # Bin to images, partition by partition.
+        meta = pd.DataFrame(columns=data.columns).astype(dtype=data.dtypes)
+        data = dd.map_partitions(
+            make_images, data, image_size, images, meta=meta, enforce_metadata=False
+        )
+
+        print("Computing the binned images.")
+        # Use multi-threading, rather than multi-processing.
+        with Client(processes=False):
+            compute_with_progress(data)
+
+    print("Transferring the images to the output file.")
+    with h5py.File(output_file, write_mode) as f:
+        zarr.copy_all(zarr.open(images.store), f, **Bitshuffle())
+
+    # Delete the Zarr store.
+    images.store.clear()
+
+    print(f"Images written to\n\t{output_nexus or output_file}")
+
+
 parser = argparse.ArgumentParser(description=__doc__, parents=[version_parser])
 subparsers = parser.add_subparsers(
     help="Choose the manner in which to create images.",
@@ -603,6 +714,16 @@ def multiple_sequences_cli(args):
 )
 parser_multiple_sequences.set_defaults(func=multiple_sequences_cli)
 
+parser_serial = subparsers.add_parser(
+    "serial",
+    description="Bin events into images, gated with trigger signals.\n\n"
+    "Events will be binned into as many images as there are gate signals, one image "
+    "per gate.  Each 'gate-open' signal is taken as the start of an exposure and the "
+    "next 'gate-close' signal is taken as the end of the exposure.",
+    parents=[version_parser, input_parser, image_output_parser, gate_parser],
+)
+parser_serial.set_defaults(func=gated_images_cli)
+
 
 def main(args=None):
     """Perform the image binning with a user-specified sub-command."""

From 8ce2091f596eb47aae4af3cc7c98bfc6bc008d92 Mon Sep 17 00:00:00 2001
From: Ben Williams <benjaminhwilliams@users.noreply.github.com>
Date: Thu, 24 Nov 2022 21:49:29 +0000
Subject: [PATCH 02/30] Rationalise checks for parsers that give no help

---
 tests/test_command_line.py | 52 ++++++++++++++------------------------
 1 file changed, 19 insertions(+), 33 deletions(-)

diff --git a/tests/test_command_line.py b/tests/test_command_line.py
index 2c47bba9..36984b49 100644
--- a/tests/test_command_line.py
+++ b/tests/test_command_line.py
@@ -13,6 +13,7 @@
     check_output_file,
     data_files,
     exposure_parser,
+    gate_parser,
     image_output_parser,
     image_size,
     input_parser,
@@ -74,6 +75,24 @@ def test_data_files(dummy_data_transient):
         data_files(dummy_data_transient, stem)
 
 
+no_help_parameters = [
+    (version_parser, []),
+    (input_parser, ["some/dummy/path/to/file_name_meta.h5"]),
+    (image_output_parser, []),
+    (exposure_parser, ["-e", ".1"]),
+    (gate_parser, ["-g", "TTL-rising"]),
+]
+
+
+@pytest.mark.parametrize(("parser", "req_arguments"), no_help_parameters)
+def test_no_help(capsys, parser: argparse.ArgumentParser, req_arguments: list[str]):
+    """Check that this parser does not introduce a help flag."""
+    for flag in "-h", "--help":
+        with pytest.raises(SystemExit, match="2"):
+            parser.parse_args([*req_arguments, flag])
+        assert f"error: unrecognized arguments: {flag}" in capsys.readouterr().err
+
+
 def test_version_parser(capsys):
     """Test that the version parser gives the correct behaviour."""
     for flag in "--version", "-V":
@@ -87,13 +106,6 @@ def test_version_parser_optional():
     assert version_parser.parse_args([]) == argparse.Namespace()
 
 
-def test_version_parser_no_help(capsys):
-    """Check that the version parser does not introduce a help flag."""
-    with pytest.raises(SystemExit, match="2"):
-        version_parser.parse_args(["-h"])
-    assert "error: unrecognized arguments: -h" in capsys.readouterr().err
-
-
 @pytest.mark.parametrize(
     "filename", ("dummy_meta.h5", "dummy_1.h5", "dummy_0001.h5", "dummy.nxs")
 )
@@ -243,16 +255,6 @@ def test_input_parser_cwd(run_in_tmp_path, filename):
     assert args.stem == "dummy"
 
 
-def test_input_parser_no_help(capsys):
-    """Check that the input parser does not introduce a help flag."""
-    directory = "some/dummy/path/to"
-    stem = "file_name"
-    for flag in "-h", "--help":
-        with pytest.raises(SystemExit, match="2"):
-            input_parser.parse_args([f"{directory}/{stem}_meta.h5", flag])
-        assert f"error: unrecognized arguments: {flag}" in capsys.readouterr().err
-
-
 def test_image_size():
     """Test unpacking an image size tuple from a comma-separated string of integers."""
     for size in "1,2", "1, 2", "1 ,2", "1 , 2", "(1,2)", "'1,2'", '"1,2"', "'\"(1,2'\"":
@@ -331,14 +333,6 @@ def test_image_output_parser_malformed_image_size(capsys):
         )
 
 
-def test_image_output_parser_no_help(capsys):
-    """Check that the output/image size parser does not introduce a help flag."""
-    for flag in "-h", "--help":
-        with pytest.raises(SystemExit, match="2"):
-            image_output_parser.parse_args([flag])
-        assert f"error: unrecognized arguments: {flag}" in capsys.readouterr().err
-
-
 def test_units_of_time():
     """Test the utility for applying a default unit to a quantity."""
     # Check that a dimensionless input quantity defaults to seconds.
@@ -452,11 +446,3 @@ def test_exposure_time_mutually_exclusive(capsys):
         "error: argument -e/--exposure-time: not allowed with argument -n/--num-images"
         in capsys.readouterr().err
     )
-
-
-def test_exposure_time_no_help(capsys):
-    """Check that this parser does not introduce a help flag."""
-    for flag in "-h", "--help":
-        with pytest.raises(SystemExit, match="2"):
-            exposure_parser.parse_args(["-e", ".1", flag])
-        assert f"error: unrecognized arguments: {flag}" in capsys.readouterr().err

From 79d1e8c0a3571d88b678fa8bad394b5e3a10fe70 Mon Sep 17 00:00:00 2001
From: Ben Williams <benjaminhwilliams@users.noreply.github.com>
Date: Fri, 25 Nov 2022 18:18:42 +0000
Subject: [PATCH 03/30] Fix some misuse of Dask objects

---
 src/tristan/command_line/images.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/tristan/command_line/images.py b/src/tristan/command_line/images.py
index 047f814e..46901188 100644
--- a/src/tristan/command_line/images.py
+++ b/src/tristan/command_line/images.py
@@ -573,8 +573,8 @@ def gated_images_cli(args):
             f"Note that signals before the shutter open time are ignored."
         )
 
-    open_times.sort_values(inplace=True)
-    close_times.sort_values(inplace=True)
+    open_times = np.sort(open_times)
+    close_times = np.sort(close_times)
 
     num_images = open_times.size
 
@@ -614,7 +614,7 @@ def gated_images_cli(args):
         open_times = da.take(open_times, open_index)
         close_times = da.take(close_times, close_index)
         data = valid_events(data, open_times, close_times)
-        data.drop(columns=event_time_key, inplace=True)
+        data = data.drop(columns=event_time_key)
 
         # Convert the event IDs to a form that is suitable for a NumPy bincount.
         data[event_location_key] = pixel_index(data[event_location_key], image_size)

From 62e82b2c00a64440b062c47ab68e7645a9f8d448 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <54588199+noemifrisina@users.noreply.github.com>
Date: Fri, 10 Feb 2023 23:11:23 +0000
Subject: [PATCH 04/30] Use new copy tool for serial crystallography data

---
 src/tristan/command_line/images.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/tristan/command_line/images.py b/src/tristan/command_line/images.py
index 2c27fc03..dca76661 100644
--- a/src/tristan/command_line/images.py
+++ b/src/tristan/command_line/images.py
@@ -586,7 +586,7 @@ def gated_images_cli(args):
     if input_nexus.exists():
         try:
             # Write output NeXus file if we have an input NeXus file.
-            output_nexus = CopyTristanNexus.multiple_images_nexus(
+            output_nexus = CopyTristanNexus.serial_images_nexus(
                 output_file,
                 input_nexus,
                 nbins=num_images,

From 7705aa340c1d99d890d07f20925e5d1cb40ec046 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <54588199+noemifrisina@users.noreply.github.com>
Date: Fri, 10 Feb 2023 23:13:22 +0000
Subject: [PATCH 05/30] Pin nexgen to latest version to get the serial tools
 working

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 312dd1c9..fbeeae8f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -32,7 +32,7 @@ install_requires =
     dask[array,diagnostics,distributed] != 2021.3.*
     h5py
     hdf5plugin
-    nexgen >= 0.6.8
+    nexgen >= 0.6.20
     numpy
     pandas
     pint

From 08d0c9d14fbca7c63eacfee3e0c629930630797a Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Fri, 17 Feb 2023 15:56:26 +0000
Subject: [PATCH 06/30] Add first and last trigger timestamp and warn if they
 happen before/after shutter

---
 .../diagnostics/find_trigger_intervals.py      | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/src/tristan/diagnostics/find_trigger_intervals.py b/src/tristan/diagnostics/find_trigger_intervals.py
index e0bf912c..c21fd0d0 100644
--- a/src/tristan/diagnostics/find_trigger_intervals.py
+++ b/src/tristan/diagnostics/find_trigger_intervals.py
@@ -273,6 +273,8 @@ def main(args):
             logger.info("TTL")
             logger.info(f"Found {len(v['TTL re'])} rising edges.\n")
             if len(v["TTL re"]) > 0:
+                logger.info(f"First TTL rising edge timestamp: {v['TTL re'][0]:.4f} .")
+                logger.info(f"Last TTL rising edge timestamp: {v['TTL re'][-1]:.4f} .")
                 d = [i - v["TTL re"][n - 1] for n, i in enumerate(v["TTL re"])][1:]
                 d_avg = np.average(d) if len(d) else np.nan
                 logger.info(
@@ -321,6 +323,22 @@ def main(args):
                     logger.info(
                         f"Found {len(v['SYNC re'])} rising edges and {len(v['SYNC fe'])} falling edges."
                     )
+                    logger.info(
+                        f"First SYNC rising edge timestamp: {v['SYNC re'][0]:.4f} ."
+                    )
+                    # logger.info(f"First SYNC falling edge timestamp: {v['SYNC fe'][0]:.4f} .")
+                    # logger.info(f"Last SYNC rising edge timestamp: {v['SYNC re'][-1]:.4f} .")
+                    logger.info(
+                        f"Last SYNC falling edge timestamp: {v['SYNC fe'][-1]:.4f} ."
+                    )
+                    if v["SYNC re"][0] < shutters[0][0]:
+                        logger.warning(
+                            "First SYNC rising edge was recorded before the shutter open signal!"
+                        )
+                    if v["SYNC fe"][-1] < shutters[1][0]:
+                        logger.warning(
+                            "Last SYNC falling edge was recorded after the shutter close signal!"
+                        )
                     diff4 = [b - a for a, b in zip(v["SYNC re"], v["SYNC fe"])]
                     avg4 = np.average(diff4) if len(diff4) else np.nan
                     logger.info(

From 1fd29dec984626fd074629c16af3e26b841127d8 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Fri, 17 Feb 2023 16:20:21 +0000
Subject: [PATCH 07/30] Fix typo

---
 src/tristan/diagnostics/find_trigger_intervals.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/tristan/diagnostics/find_trigger_intervals.py b/src/tristan/diagnostics/find_trigger_intervals.py
index c21fd0d0..dfee47bf 100644
--- a/src/tristan/diagnostics/find_trigger_intervals.py
+++ b/src/tristan/diagnostics/find_trigger_intervals.py
@@ -335,7 +335,7 @@ def main(args):
                         logger.warning(
                             "First SYNC rising edge was recorded before the shutter open signal!"
                         )
-                    if v["SYNC fe"][-1] < shutters[1][0]:
+                    if v["SYNC fe"][-1] > shutters[1][0]:
                         logger.warning(
                             "Last SYNC falling edge was recorded after the shutter close signal!"
                         )

From ef8317162315f0f9f4f4fc3262b7d47a2cd5c767 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Tue, 21 Feb 2023 09:59:53 +0000
Subject: [PATCH 08/30] Print also timestamp difference between shutters and
 signal to see just how small the interval is

---
 CHANGELOG.md                                      | 1 +
 src/tristan/diagnostics/find_trigger_intervals.py | 6 ++++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index dac728d8..71606604 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ##
 - Fixed the axis dimensions for `images pp`.
+- Added timestamp check and warning on triggers if they happen before/after shutters in `find-tristan-triggers`.
 
 ## 0.2.1
 - Added dagnostic tool `valid-events` for checking that there are events recorded after the shutter open signal in case the binned image is blank(asynchronicity issue). Also, a couple of small improvements on the other diagnostic tools.
diff --git a/src/tristan/diagnostics/find_trigger_intervals.py b/src/tristan/diagnostics/find_trigger_intervals.py
index dfee47bf..8b7ce894 100644
--- a/src/tristan/diagnostics/find_trigger_intervals.py
+++ b/src/tristan/diagnostics/find_trigger_intervals.py
@@ -333,11 +333,13 @@ def main(args):
                     )
                     if v["SYNC re"][0] < shutters[0][0]:
                         logger.warning(
-                            "First SYNC rising edge was recorded before the shutter open signal!"
+                            "First SYNC rising edge was recorded before the shutter open signal! \n"
+                            f"Timestamp difference: {shutters[0][0] - v['SYNC re'][0]} s."
                         )
                     if v["SYNC fe"][-1] > shutters[1][0]:
                         logger.warning(
-                            "Last SYNC falling edge was recorded after the shutter close signal!"
+                            "Last SYNC falling edge was recorded after the shutter close signal! \n"
+                            f"Timestamp difference: {v['SYNC fe'][-1] - shutters[1][0]} s."
                         )
                     diff4 = [b - a for a, b in zip(v["SYNC re"], v["SYNC fe"])]
                     avg4 = np.average(diff4) if len(diff4) else np.nan

From 291b9e939405297db35f294567beb307a3af1bf1 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Tue, 21 Feb 2023 10:51:49 +0000
Subject: [PATCH 09/30] Tidy up printed messages

---
 .../diagnostics/find_trigger_intervals.py        | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/tristan/diagnostics/find_trigger_intervals.py b/src/tristan/diagnostics/find_trigger_intervals.py
index 8b7ce894..27cf8b54 100644
--- a/src/tristan/diagnostics/find_trigger_intervals.py
+++ b/src/tristan/diagnostics/find_trigger_intervals.py
@@ -237,8 +237,8 @@ def main(args):
             logger.info(f"--- {k} ---")
             logger.info("SHUTTERS")
             if len(shutters[0]) > 0 and len(shutters[1]) > 0:
-                logger.info(f"Shutter open timestamp: {shutters[0][0]:.4f}")
-                logger.info(f"Shutter close timestamp: {shutters[1][0]:.4f}")
+                logger.info(f"Shutter open timestamp: {shutters[0][0]:.4f}.")
+                logger.info(f"Shutter close timestamp: {shutters[1][0]:.4f}.")
                 diff0 = shutters[1][0] - shutters[0][0]
                 logger.info(
                     f"Total time between shutter opening and closing: {diff0:.4f} s."
@@ -246,10 +246,10 @@ def main(args):
             elif len(shutters[0]) == 0 or len(shutters[1]) == 0:
                 logger.warning("Missing shutter information!")
                 logger.warning(
-                    f"Number of shutter open timestamps found: {len(shutters[0])}"
+                    f"Number of shutter open timestamps found: {len(shutters[0])}."
                 )
                 logger.warning(
-                    f"Number of shutter close timestamps found: {len(shutters[1])}"
+                    f"Number of shutter close timestamps found: {len(shutters[1])}."
                 )
             logger.info("LVDS")
             if len(v["LVDS re"]) > 0 and len(v["LVDS fe"]) > 0:
@@ -324,12 +324,12 @@ def main(args):
                         f"Found {len(v['SYNC re'])} rising edges and {len(v['SYNC fe'])} falling edges."
                     )
                     logger.info(
-                        f"First SYNC rising edge timestamp: {v['SYNC re'][0]:.4f} ."
+                        f"First SYNC rising edge timestamp: {v['SYNC re'][0]:.4f}."
                     )
                     # logger.info(f"First SYNC falling edge timestamp: {v['SYNC fe'][0]:.4f} .")
                     # logger.info(f"Last SYNC rising edge timestamp: {v['SYNC re'][-1]:.4f} .")
                     logger.info(
-                        f"Last SYNC falling edge timestamp: {v['SYNC fe'][-1]:.4f} ."
+                        f"Last SYNC falling edge timestamp: {v['SYNC fe'][-1]:.4f}."
                     )
                     if v["SYNC re"][0] < shutters[0][0]:
                         logger.warning(
@@ -344,13 +344,13 @@ def main(args):
                     diff4 = [b - a for a, b in zip(v["SYNC re"], v["SYNC fe"])]
                     avg4 = np.average(diff4) if len(diff4) else np.nan
                     logger.info(
-                        f"Average time interval between SYNC re and fe: {avg4:.4f} s"
+                        f"Average time interval between SYNC re and fe: {avg4:.4f} s."
                     )
                     if len(v["TTL re"]) == len(v["SYNC re"]):
                         diff5 = [b - a for a, b in zip(v["TTL re"], v["SYNC re"])]
                         avg5 = np.average(diff5) if len(diff5) else np.nan
                         logger.info(
-                            f"Average time interval between TTL re and SYNC re: {avg5:.4f} s"
+                            f"Average time interval between TTL re and SYNC re: {avg5:.4f} s."
                         )
                     else:
                         logger.error(

From da7043df077ff0199bf603b079b7da2db75e4d14 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Tue, 21 Feb 2023 11:15:37 +0000
Subject: [PATCH 10/30] Add some docs for new tool

---
 docs/usage.rst | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/docs/usage.rst b/docs/usage.rst
index 70dfd5e2..85273dba 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -99,6 +99,29 @@ by duration, with `-i`, or by number, with `-x`.
 For example, this could be used to deconstruct a rotation data collection into several rotation datasets, each corresponding to a different pump-probe delay window.
 
 
+Serial crystallography tool (gated access)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+To bin events into images gated by trigger signals, use `images serial`, which will write one image per gate signal. Each 'gate-open' signal is taken as the start of an exposure and
+the next 'gate-close' signal is taken as the end of the exposure.
+
+This tool requires at least the rising edge of the trigger signal, specified with `-g`, to be passed as *gate open* and will then look for the corresponding falling edge
+to be used as *gate close*. 
+
+.. code-block:: console
+
+    images serial -g SYNC-rising /path/to/file
+
+
+In some cases, it might be more useful to look at the events collected between different kinds of trigger signals, by specifying the *gate open* signal with `-g`
+and the *gate close* using the `-c` flag as in the example below.  
+
+.. code-block:: console
+
+    images serial -g TTL-rising -c SYNC-falling /path/to/file
+
+
+
 Apply the flatfield correction
 ==============================
 

From 0d3c39517852e6ab58c4bb514e616654b03688f8 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Tue, 21 Feb 2023 13:50:35 +0000
Subject: [PATCH 11/30] Hack to use the shutter open/close if first/last
 trigger signal is missing

---
 src/tristan/command_line/images.py | 46 ++++++++++++++++++++++++------
 src/tristan/data.py                |  9 +++++-
 2 files changed, 46 insertions(+), 9 deletions(-)

diff --git a/src/tristan/command_line/images.py b/src/tristan/command_line/images.py
index dca76661..0c271133 100644
--- a/src/tristan/command_line/images.py
+++ b/src/tristan/command_line/images.py
@@ -561,8 +561,10 @@ def gated_images_cli(args):
             start, end = find_start_end(cues_data)
 
         print("Finding gate signal times.")
+        # Here we assume no synchronization issues:
+        # falling edges always recorded after rising edges.
         open_times = cue_times(cues_data, gate_open, after=start)
-        close_times = cue_times(cues_data, gate_close, after=start)
+        close_times = cue_times(cues_data, gate_close, before=end)
         with ProgressBar():
             open_times, close_times = dask.compute(open_times, close_times)
 
@@ -570,17 +572,45 @@ def gated_images_cli(args):
         sys.exit(f"Could not find a '{cues[gate_open]}' signal.")
     if not close_times.size:
         sys.exit(f"Could not find a '{cues[gate_close]}' signal.")
-    if not open_times.size == close_times.size:
-        sys.exit(
-            "Found a non-matching number of gate open and close signals:\n\t"
-            f"Number of '{cues[gate_open]}' signals: {open_times.size}\n\t"
-            f"Number of '{cues[gate_close]}' signals: {close_times.size}\n"
-            f"Note that signals before the shutter open time are ignored."
-        )
 
     open_times = np.sort(open_times)
     close_times = np.sort(close_times)
 
+    if not open_times.size == close_times.size:
+        # If size difference is just one, look for missing one right before/after
+        # sutter and use shutter timestamp as first/last gate
+        if abs(open_times.size - close_times.size) > 1:
+            sys.exit(
+                "Found a non-matching number of gate open and close signals:\n\t"
+                f"Number of '{cues[gate_open]}' signals: {open_times.size}\n\t"
+                f"Number of '{cues[gate_close]}' signals: {close_times.size}\n"
+                f"Note that signals before the shutter open time are ignored."
+            )
+        else:
+            if open_times[-1] > close_times[-1]:
+                print(
+                    "WARNING! \n\t"
+                    f"Missing last '{cues[gate_close]}' signal.\n\t"
+                    f"Shutter close timestamp will be used instead for last image."
+                )
+                # Append shutter close to close_times
+                close_times = np.append(close_times, end)
+            elif open_times[0] > close_times[0]:
+                print(
+                    "WARNING! \n\t"
+                    f"Missing first '{cues[gate_open]}' signal.\n\t"
+                    f"Shutter open timestamp will be used instead for last image."
+                )
+                # Insert shutter open to open times
+                open_times = np.insert(open_times, 0, start)
+            else:
+                sys.exit(
+                    "Found a non-matching number of gate open and close signals:\n\t"
+                    f"Number of '{cues[gate_open]}' signals: {open_times.size}\n\t"
+                    f"Number of '{cues[gate_close]}' signals: {close_times.size}\n"
+                    # f"Note that signals before the shutter open time are ignored."
+                )
+
     num_images = open_times.size
 
     if input_nexus.exists():
diff --git a/src/tristan/data.py b/src/tristan/data.py
index 3e7dacd8..f6330a99 100644
--- a/src/tristan/data.py
+++ b/src/tristan/data.py
@@ -146,7 +146,12 @@ def first_cue_time(
         return data[cue_time_key].loc[first_index]
 
 
-def cue_times(data: dd.DataFrame, message: int, after: int | None = None) -> da.Array:
+def cue_times(
+    data: dd.DataFrame,
+    message: int,
+    after: int | None = None,
+    before: int | None = None,
+) -> da.Array:
     """
     Find the timestamps of all instances of a cue message in a Tristan data set.
 
@@ -165,6 +170,8 @@ def cue_times(data: dd.DataFrame, message: int, after: int | None = None) -> da.
     index = data[cue_id_key] == message
     if after:
         index &= data[cue_time_key] >= after
+    if before:
+        index &= data[cue_time_key] <= before
     return da.unique(data[cue_time_key][index].values)
 
 

From e957cb7285952402fb51662b1590edb641eef175 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Tue, 21 Feb 2023 14:00:26 +0000
Subject: [PATCH 12/30] Update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 71606604..1a370b67 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@
 ##
 - Fixed the axis dimensions for `images pp`.
 - Added timestamp check and warning on triggers if they happen before/after shutters in `find-tristan-triggers`.
+- Added `images serial` for gated access binning of events.
 
 ## 0.2.1
 - Added dagnostic tool `valid-events` for checking that there are events recorded after the shutter open signal in case the binned image is blank(asynchronicity issue). Also, a couple of small improvements on the other diagnostic tools.

From e1682e8ef11fa13743cc1bd4bdd6205f0f067788 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 10:46:48 +0100
Subject: [PATCH 13/30] Try to make the gated_access work

---
 src/tristan/command_line/images.py | 26 +++++++++++++++++++-------
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/src/tristan/command_line/images.py b/src/tristan/command_line/images.py
index 0c271133..04782fe8 100644
--- a/src/tristan/command_line/images.py
+++ b/src/tristan/command_line/images.py
@@ -612,6 +612,7 @@ def gated_images_cli(args):
                 )
 
     num_images = open_times.size
+    bins = np.linspace(0, num_images, num_images + 1, dtype=np.uint64)
 
     if input_nexus.exists():
         try:
@@ -642,20 +643,31 @@ def gated_images_cli(args):
         data = valid_events(data, start, end)
 
         # Gate the events.
-        event_times = data[event_time_key].values
+        event_times = data[event_time_key].astype(np.int64).values
         open_index = da.digitize(event_times, open_times) - 1
         close_index = da.digitize(event_times, close_times) - 1
-        data["time_bin"] = open_index
-        open_times = da.take(open_times, open_index)
-        close_times = da.take(close_times, close_index)
-        data = valid_events(data, open_times, close_times)
-        data = data.drop(columns=event_time_key)
+        # Look for events that happen after gate open and before gate close
+        after_open = event_times - da.take(open_times, open_index)
+        before_close = da.take(close_times, close_index) - event_times
+        # Eliminate invalid events.
+        # Valid only if both before and after are positive
+        valid = (after_open > 0) & (before_close > 0)
+        valid = dd.from_dask_array(valid, index=data.index)
 
         # Convert the event IDs to a form that is suitable for a NumPy bincount.
         data[event_location_key] = pixel_index(data[event_location_key], image_size)
 
+        columns = event_location_key, "time_bin"
+        dtypes = data.dtypes
+        dtypes["time_bin"] = dtypes.pop(event_time_key)
+
+        meta = pd.DataFrame(columns=columns).astype(dtype=dtypes)
+        # Enumerate the image in the stack to which each event belongs
+        data = data.map_partitions(find_time_bins, bins=bins, meta=meta)
+        data["time_bin"] = open_index
+        data = data[valid]
+
         # Bin to images, partition by partition.
-        meta = pd.DataFrame(columns=data.columns).astype(dtype=data.dtypes)
         data = dd.map_partitions(
             make_images, data, image_size, images, meta=meta, enforce_metadata=False
         )

From 7183e3c48a64f1ed901a3bbb201415eb16192faa Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 11:07:08 +0100
Subject: [PATCH 14/30] Update versions for docs

---
 .readthedocs.yaml    | 2 +-
 requirements.txt     | 2 +-
 requirements_dev.txt | 2 +-
 requirements_doc.txt | 4 ++--
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 093a84c1..8746836f 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -11,7 +11,7 @@ sphinx:
 
 # Set the version of Python and optionally declare the requirements required to build your docs
 python:
-  version: '3.8'
+  version: '3.10'
   install:
   - method: pip
     path: .
diff --git a/requirements.txt b/requirements.txt
index 48376605..1fbf961e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,7 +2,7 @@ dask==2022.11.1
 distributed==2022.11.1
 h5py==3.7.0
 hdf5plugin==3.3.1
-nexgen==0.6.14
+nexgen==0.6.23
 numpy==1.23.5
 pandas==1.5.2
 Pint==0.20.1
diff --git a/requirements_dev.txt b/requirements_dev.txt
index 4c9170d5..1f894323 100644
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -2,7 +2,7 @@ dask==2022.11.1
 distributed==2022.11.1
 h5py==3.7.0
 hdf5plugin==3.3.1
-nexgen==0.6.14
+nexgen==0.6.23
 numpy==1.23.5
 pandas==1.5.2
 Pint==0.20.1
diff --git a/requirements_doc.txt b/requirements_doc.txt
index 45d2f55e..e9f78686 100644
--- a/requirements_doc.txt
+++ b/requirements_doc.txt
@@ -2,10 +2,10 @@ dask==2022.11.1
 distributed==2022.11.1
 h5py==3.7.0
 hdf5plugin==3.3.1
-nexgen==0.6.14
+nexgen==0.6.25
 numpy==1.23.5
 pandas==1.5.2
 Pint==0.20.1
-Sphinx==4.5.0
+Sphinx==7.0.0
 sphinx-rtd-theme==1.0.0
 zarr==2.13.3

From 25c2b085c7cd5faf767259886f798319af2aa9dc Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 11:10:42 +0100
Subject: [PATCH 15/30] Update versions for docs - try again

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 8746836f..093a84c1 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -11,7 +11,7 @@ sphinx:
 
 # Set the version of Python and optionally declare the requirements required to build your docs
 python:
-  version: '3.10'
+  version: '3.8'
   install:
   - method: pip
     path: .

From 36ff926e5ece192d30de831788549a8267fc751b Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 11:13:48 +0100
Subject: [PATCH 16/30] Update versions for docs - try again part 2

---
 requirements.txt     | 2 +-
 requirements_dev.txt | 2 +-
 requirements_doc.txt | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 1fbf961e..ba618e54 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,7 @@
 dask==2022.11.1
 distributed==2022.11.1
 h5py==3.7.0
-hdf5plugin==3.3.1
+hdf5plugin==4.0.1
 nexgen==0.6.23
 numpy==1.23.5
 pandas==1.5.2
diff --git a/requirements_dev.txt b/requirements_dev.txt
index 1f894323..39173e44 100644
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -1,7 +1,7 @@
 dask==2022.11.1
 distributed==2022.11.1
 h5py==3.7.0
-hdf5plugin==3.3.1
+hdf5plugin==4.0.1
 nexgen==0.6.23
 numpy==1.23.5
 pandas==1.5.2
diff --git a/requirements_doc.txt b/requirements_doc.txt
index e9f78686..de419b60 100644
--- a/requirements_doc.txt
+++ b/requirements_doc.txt
@@ -1,7 +1,7 @@
 dask==2022.11.1
 distributed==2022.11.1
 h5py==3.7.0
-hdf5plugin==3.3.1
+hdf5plugin==4.0.1
 nexgen==0.6.25
 numpy==1.23.5
 pandas==1.5.2

From f1deeab9eb8c7e8d6e89446794193ba1d7fa065d Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 11:15:55 +0100
Subject: [PATCH 17/30] Fix typo

---
 requirements_doc.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements_doc.txt b/requirements_doc.txt
index de419b60..6b0c7b5f 100644
--- a/requirements_doc.txt
+++ b/requirements_doc.txt
@@ -2,7 +2,7 @@ dask==2022.11.1
 distributed==2022.11.1
 h5py==3.7.0
 hdf5plugin==4.0.1
-nexgen==0.6.25
+nexgen==0.6.23
 numpy==1.23.5
 pandas==1.5.2
 Pint==0.20.1

From 1aafa36fc3bc0a0e1ae83dee5def52f4f3bcab99 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 11:20:25 +0100
Subject: [PATCH 18/30] Update versions for docs - try again part 3

---
 requirements_doc.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements_doc.txt b/requirements_doc.txt
index 6b0c7b5f..d3b33ef9 100644
--- a/requirements_doc.txt
+++ b/requirements_doc.txt
@@ -7,5 +7,5 @@ numpy==1.23.5
 pandas==1.5.2
 Pint==0.20.1
 Sphinx==7.0.0
-sphinx-rtd-theme==1.0.0
+sphinx-rtd-theme==1.2.0
 zarr==2.13.3

From a7558632d0b8849d7bde41897947f0be5d11c9cb Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 11:22:46 +0100
Subject: [PATCH 19/30] Update versions for docs - try again part 4

---
 requirements_doc.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements_doc.txt b/requirements_doc.txt
index d3b33ef9..cbd90bae 100644
--- a/requirements_doc.txt
+++ b/requirements_doc.txt
@@ -6,6 +6,6 @@ nexgen==0.6.23
 numpy==1.23.5
 pandas==1.5.2
 Pint==0.20.1
-Sphinx==7.0.0
+Sphinx==6.2.0
 sphinx-rtd-theme==1.2.0
 zarr==2.13.3

From 766a955639e6dcc6a5bd99bcb7ce177b166f31ca Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 11:40:36 +0100
Subject: [PATCH 20/30] Update versions for docs - try again part 5

---
 .azure-pipelines/azure-pipelines.yml | 2 +-
 .readthedocs.yaml                    | 2 +-
 src/tristan/command_line/images.py   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.azure-pipelines/azure-pipelines.yml b/.azure-pipelines/azure-pipelines.yml
index cd233c27..5d47006c 100644
--- a/.azure-pipelines/azure-pipelines.yml
+++ b/.azure-pipelines/azure-pipelines.yml
@@ -106,7 +106,7 @@ stages:
     - task: UsePythonVersion@0
       displayName: Set up python
       inputs:
-        versionSpec: 3.8
+        versionSpec: 3.10
 
     - task: DownloadBuildArtifacts@0
       displayName: Get pre-built package
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 093a84c1..8746836f 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -11,7 +11,7 @@ sphinx:
 
 # Set the version of Python and optionally declare the requirements required to build your docs
 python:
-  version: '3.8'
+  version: '3.10'
   install:
   - method: pip
     path: .
diff --git a/src/tristan/command_line/images.py b/src/tristan/command_line/images.py
index 04782fe8..7ebfa214 100644
--- a/src/tristan/command_line/images.py
+++ b/src/tristan/command_line/images.py
@@ -651,7 +651,7 @@ def gated_images_cli(args):
         before_close = da.take(close_times, close_index) - event_times
         # Eliminate invalid events.
         # Valid only if both before and after are positive
-        valid = (after_open > 0) & (before_close > 0)
+        valid = (after_open >= 0) & (before_close > 0)
         valid = dd.from_dask_array(valid, index=data.index)
 
         # Convert the event IDs to a form that is suitable for a NumPy bincount.

From 66244e4e1ee35d153aa8bb47fc26da7a376d5417 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 11:42:08 +0100
Subject: [PATCH 21/30] Try removing deprecated version from docs config file

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 8746836f..f53ef02b 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -11,7 +11,7 @@ sphinx:
 
 # Set the version of Python and optionally declare the requirements required to build your docs
 python:
-  version: '3.10'
+  #version: '3.10'
   install:
   - method: pip
     path: .

From c80c22ebd0de9624ba73de37bb26d96bc8a820b0 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 12:01:25 +0100
Subject: [PATCH 22/30] Update readthedocs config file

---
 .readthedocs.yaml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index f53ef02b..c077f19d 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -5,13 +5,19 @@
 # Required
 version: 2
 
+# Set the version of python and other tools
+build:
+  os: ubuntu-22.04
+  tools:
+    python: '3.10'
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
 # Set the version of Python and optionally declare the requirements required to build your docs
 python:
-  #version: '3.10'
+  #version: '3.8'
   install:
   - method: pip
     path: .

From d8848836ab2468f53003ad57632705ca0ad16a59 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 13:59:26 +0100
Subject: [PATCH 23/30] Fix typo

---
 src/tristan/command_line/images.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/tristan/command_line/images.py b/src/tristan/command_line/images.py
index 7ebfa214..96f1edb5 100644
--- a/src/tristan/command_line/images.py
+++ b/src/tristan/command_line/images.py
@@ -645,7 +645,7 @@ def gated_images_cli(args):
         # Gate the events.
         event_times = data[event_time_key].astype(np.int64).values
         open_index = da.digitize(event_times, open_times) - 1
-        close_index = da.digitize(event_times, close_times) - 1
+        close_index = da.digitize(event_times, close_times)
         # Look for events that happen after gate open and before gate close
         after_open = event_times - da.take(open_times, open_index)
         before_close = da.take(close_times, close_index) - event_times

From 2b230df108cb3813cfca2bd1ba3a3b28cf0dba98 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 14:03:18 +0100
Subject: [PATCH 24/30] Fix number of bins

---
 src/tristan/command_line/images.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/tristan/command_line/images.py b/src/tristan/command_line/images.py
index 96f1edb5..f9c611ed 100644
--- a/src/tristan/command_line/images.py
+++ b/src/tristan/command_line/images.py
@@ -612,7 +612,7 @@ def gated_images_cli(args):
                 )
 
     num_images = open_times.size
-    bins = np.linspace(0, num_images, num_images + 1, dtype=np.uint64)
+    bins = np.linspace(0, num_images - 1, num_images, dtype=np.uint64)
 
     if input_nexus.exists():
         try:

From 1178a60c9f768bfa4ea76904fa8fcb8d90ac7639 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 14:50:52 +0100
Subject: [PATCH 25/30] Small changes

---
 src/tristan/command_line/images.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/tristan/command_line/images.py b/src/tristan/command_line/images.py
index f9c611ed..b3b3ea21 100644
--- a/src/tristan/command_line/images.py
+++ b/src/tristan/command_line/images.py
@@ -599,7 +599,7 @@ def gated_images_cli(args):
                 print(
                     "WARNING! \n\t"
                     f"Missing first '{cues[gate_open]}' signal.\n\t"
-                    f"Shutter open timestamp will be used instead for last image."
+                    f"Shutter open timestamp will be used instead for first image."
                 )
                 # Insert shutter open to open times
                 open_times = np.insert(open_times, 0, start)
@@ -612,7 +612,7 @@ def gated_images_cli(args):
                 )
 
     num_images = open_times.size
-    bins = np.linspace(0, num_images - 1, num_images, dtype=np.uint64)
+    bins = np.linspace(0, num_images, num_images + 1, dtype=np.uint64)
 
     if input_nexus.exists():
         try:
@@ -647,11 +647,12 @@ def gated_images_cli(args):
         open_index = da.digitize(event_times, open_times) - 1
         close_index = da.digitize(event_times, close_times)
         # Look for events that happen after gate open and before gate close
-        after_open = event_times - da.take(open_times, open_index)
-        before_close = da.take(close_times, close_index) - event_times
+        # after_open = event_times - da.take(open_times, open_index)
+        # before_close = da.take(close_times, close_index) - event_times
         # Eliminate invalid events.
         # Valid only if both before and after are positive
-        valid = (after_open >= 0) & (before_close > 0)
+        # valid = (after_open >= 0) & (before_close > 0)
+        valid = open_index == close_index
         valid = dd.from_dask_array(valid, index=data.index)
 
         # Convert the event IDs to a form that is suitable for a NumPy bincount.

From ba947f57043fa297c0bccf40ac92f7c8f3218f1a Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 15:14:53 +0100
Subject: [PATCH 26/30] Small changes

---
 docs/api.rst   | 6 ++++++
 docs/usage.rst | 5 +++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/docs/api.rst b/docs/api.rst
index c5dddd8d..a84e8bae 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -2,6 +2,9 @@
 API
 ===
 
+General
+=======
+
 .. automodule:: tristan
     :members:
     :show-inheritance:
@@ -25,6 +28,9 @@ Data
 Diagnostics API
 ===============
 
+General
+=======
+
 .. automodule:: tristan.diagnostics
     :members:
 
diff --git a/docs/usage.rst b/docs/usage.rst
index 85273dba..76380860 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -106,7 +106,7 @@ To bin events into images gated by trigger signals, use `images serial`, which w
 the next 'gate-close' signal is taken as the end of the exposure.
 
 This tool requires at least the rising edge of the trigger signal, specified with `-g`, to be passed as *gate open* and will then look for the corresponding falling edge
-to be used as *gate close*. 
+to be used as *gate close*.
 
 .. code-block:: console
 
@@ -114,7 +114,7 @@ to be used as *gate close*.
 
 
 In some cases, it might be more useful to look at the events collected between different kinds of trigger signals, by specifying the *gate open* signal with `-g`
-and the *gate close* using the `-c` flag as in the example below.  
+and the *gate close* using the `-c` flag as in the example below.
 
 .. code-block:: console
 
@@ -122,6 +122,7 @@ and the *gate close* using the `-c` flag as in the example below.
 
 
 
+==============================
 Apply the flatfield correction
 ==============================
 

From c827abd43b6704654bccece6c65ce8995609270f Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 10 May 2023 15:53:39 +0100
Subject: [PATCH 27/30] Tidy up a bit

---
 .readthedocs.yaml                  | 1 -
 src/tristan/command_line/images.py | 9 ++-------
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index c077f19d..416a0faf 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -17,7 +17,6 @@ sphinx:
 
 # Set the version of Python and optionally declare the requirements required to build your docs
 python:
-  #version: '3.8'
   install:
   - method: pip
     path: .
diff --git a/src/tristan/command_line/images.py b/src/tristan/command_line/images.py
index b3b3ea21..2b65778d 100644
--- a/src/tristan/command_line/images.py
+++ b/src/tristan/command_line/images.py
@@ -578,7 +578,7 @@ def gated_images_cli(args):
 
     if not open_times.size == close_times.size:
         # If size difference is just one, look for missing one right before/after
-        # sutter and use shutter timestamp as first/last gate
+        # shutters and use shutter open/close timestamp as first/last gate
         if abs(open_times.size - close_times.size) > 1:
             sys.exit(
                 "Found a non-matching number of gate open and close signals:\n\t"
@@ -608,7 +608,6 @@ def gated_images_cli(args):
                     "Found a non-matching number of gate open and close signals:\n\t"
                     f"Number of '{cues[gate_open]}' signals: {open_times.size}\n\t"
                     f"Number of '{cues[gate_close]}' signals: {close_times.size}\n"
-                    # f"Note that signals before the shutter open time are ignored."
                 )
 
     num_images = open_times.size
@@ -647,11 +646,7 @@ def gated_images_cli(args):
         open_index = da.digitize(event_times, open_times) - 1
         close_index = da.digitize(event_times, close_times)
         # Look for events that happen after gate open and before gate close
-        # after_open = event_times - da.take(open_times, open_index)
-        # before_close = da.take(close_times, close_index) - event_times
-        # Eliminate invalid events.
-        # Valid only if both before and after are positive
-        # valid = (after_open >= 0) & (before_close > 0)
+        # Eliminate invalid events by looking at the open and close index
         valid = open_index == close_index
         valid = dd.from_dask_array(valid, index=data.index)
 

From 6c8a3a66a3dd354cd9a9f0ebe529b88b19c1ca52 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Thu, 11 May 2023 17:06:20 +0100
Subject: [PATCH 28/30] Tidy up triggers code

---
 src/tristan/diagnostics/find_trigger_intervals.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/tristan/diagnostics/find_trigger_intervals.py b/src/tristan/diagnostics/find_trigger_intervals.py
index 27cf8b54..86dbf5a3 100644
--- a/src/tristan/diagnostics/find_trigger_intervals.py
+++ b/src/tristan/diagnostics/find_trigger_intervals.py
@@ -326,8 +326,6 @@ def main(args):
                     logger.info(
                         f"First SYNC rising edge timestamp: {v['SYNC re'][0]:.4f}."
                     )
-                    # logger.info(f"First SYNC falling edge timestamp: {v['SYNC fe'][0]:.4f} .")
-                    # logger.info(f"Last SYNC rising edge timestamp: {v['SYNC re'][-1]:.4f} .")
                     logger.info(
                         f"Last SYNC falling edge timestamp: {v['SYNC fe'][-1]:.4f}."
                     )

From 7f34e7c9e342bd870749a95d9884abbaf7235968 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Thu, 11 May 2023 17:08:47 +0100
Subject: [PATCH 29/30] Clean up import pattern

---
 src/tristan/command_line/images.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/tristan/command_line/images.py b/src/tristan/command_line/images.py
index 2b65778d..9172ed0a 100644
--- a/src/tristan/command_line/images.py
+++ b/src/tristan/command_line/images.py
@@ -29,7 +29,6 @@
     find_start_end,
     find_time_bins,
     make_images,
-    valid_events,
 )
 from ..data import (
     cue_keys,
@@ -41,6 +40,7 @@
     latrd_data,
     pixel_index,
     seconds,
+    valid_events,
 )
 from . import (
     check_multiple_output_files,

From 660efe0103abb957c3578514a4ce2d9f20b4748d Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 21 Jun 2023 11:40:25 +0100
Subject: [PATCH 30/30] Update changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1a370b67..45298140 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # CHANGES
 
-##
+## 0.2.2
 - Fixed the axis dimensions for `images pp`.
 - Added timestamp check and warning on triggers if they happen before/after shutters in `find-tristan-triggers`.
 - Added `images serial` for gated access binning of events.