Beamtime code

docs/developer/serial-crystallography-on-i24/how-to/commission-a-jungfrau.md

@@ -4,7 +4,7 @@
 
 - The deployment used live both times lives in: `/dls_sw/i24/software/bluesky/jungfrau`
 - .venv in `./jungfrau_commissioning`
-- executable `jungfrau_commissioning` loads an iPython terminal
+- executable `jungfrau_commissioning` loads an iPython terminal with some more instructions
 - don't install stuff pls - this environment has dependencies which no longer exist like `python-artemis`
 - changing the code is fine
 - if you mess up the environment the dependencies can be found in current_deps.txt

jungfrau_params/acnir.json

@@ -0,0 +1,13 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 360.0,
+    "image_width_deg": 0.1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.0005,
+    "acquire_time_s": 0.0005,
+    "rotation_direction": "Negative",
+    "offset_deg": 10.0,
+    "shutter_opening_time_s": 0.3,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "data_filename": "acnir"
+}

jungfrau_params/cuhf.json

@@ -0,0 +1,13 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 360.0,
+    "image_width_deg": 0.1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.0005,
+    "acquire_time_s": 0.0005,
+    "rotation_direction": "Negative",
+    "offset_deg": 10.0,
+    "shutter_opening_time_s": 0.3,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "data_filename": "cuhf"
+}

jungfrau_params/example.json

@@ -0,0 +1,13 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 360.0,
+    "image_width_deg": 0.1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.001,
+    "acquire_time_s":  0.001,
+    "rotation_direction": "NEGATIVE",
+    "offset_deg": 10.0,
+    "shutter_opening_time_s": 0.025,
+    "storage_directory": "/dls/i24/data/2023/cm37275-4/jungfrau_commissioning",
+    "nexus_filename": "test"
+}

jungfrau_params/generic_360_rotation.json

@@ -0,0 +1,13 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 10.0,
+    "image_width_deg": 0.01,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.001,
+    "acquire_time_s":  0.001,
+    "rotation_direction": "NEGATIVE",
+    "offset_deg": 10.0,
+    "shutter_opening_time_s": 0.25,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "nexus_filename": "glass"
+}

jungfrau_params/glass.json

@@ -0,0 +1,12 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 360.0,
+    "image_width_deg": 0.1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.001,
+    "acquire_time_s":  0.001,
+    "rotation_direction": "NEGATIVE",
+    "shutter_opening_time_s": 0.6,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "nexus_filename": "glass"
+}

jungfrau_params/glycerol.json

@@ -0,0 +1,13 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 10.0,
+    "image_width_deg": 0.002,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.0005,
+    "acquire_time_s": 0.0005,
+    "rotation_direction": "Negative",
+    "offset_deg": 10.0,
+    "shutter_opening_time_s": 0.3,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "data_filename": "glycerol"
+}

jungfrau_params/insulin_1.json

@@ -0,0 +1,13 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 360.0,
+    "image_width_deg": 0.1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.0005,
+    "acquire_time_s": 0.0005,
+    "rotation_direction": "Negative",
+    "offset_deg": 10.0,
+    "shutter_opening_time_s": 0.3,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "data_filename": "insulin"
+}

jungfrau_params/insulin_1440.json

@@ -0,0 +1,13 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 1440.0,
+    "image_width_deg": 0.1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.001,
+    "acquire_time_s":  0.001,
+    "rotation_direction": "NEGATIVE",
+    "offset_deg": 10.0,
+    "shutter_opening_time_s": 0.27,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "nexus_filename": "insulin"
+}

jungfrau_params/insulin_200Hz.json

@@ -0,0 +1,13 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 360.0,
+    "image_width_deg": 1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.005,
+    "acquire_time_s": 0.005,
+    "rotation_direction": "Negative",
+    "offset_deg": 10.0,
+    "shutter_opening_time_s": 0.3,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "data_filename": "insulin"
+}

jungfrau_params/insulin_2khz.json

@@ -0,0 +1,13 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 360.0,
+    "image_width_deg": 0.1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.000475,
+    "acquire_time_s":  0.0005,
+    "rotation_direction": "NEGATIVE",
+    "offset_deg": 10.0,
+    "shutter_opening_time_s": 0.27,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "nexus_filename": "insulin"
+}

jungfrau_params/insulin_500Hz.json

@@ -0,0 +1,13 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 360.0,
+    "image_width_deg": 1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.002,
+    "acquire_time_s": 0.002,
+    "rotation_direction": "Negative",
+    "offset_deg": 10.0,
+    "shutter_opening_time_s": 0.3,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "data_filename": "insulin"
+}

jungfrau_params/manual_test.json

@@ -0,0 +1,13 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 100.0,
+    "image_width_deg": 0.1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.001,
+    "acquire_time_s":  0.001,
+    "rotation_direction": "NEGATIVE",
+    "offset_deg": 10.0,
+    "shutter_opening_time_s": 0.27,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "nexus_filename": "test_1"
+}

jungfrau_params/params_for_blank_test_run.json

@@ -0,0 +1,12 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 360.0,
+    "image_width_deg": 0.1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.001,
+    "acquire_time_s":  0.001,
+    "rotation_direction": "NEGATIVE",
+    "shutter_opening_time_s": 0.6,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "nexus_filename": "blank_test_run"
+}

jungfrau_params/peg.json

@@ -0,0 +1,12 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 360.0,
+    "image_width_deg": 0.1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.001,
+    "acquire_time_s":  0.001,
+    "rotation_direction": "NEGATIVE",
+    "shutter_opening_time_s": 0.6,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "nexus_filename": "glycerol"
+}

jungfrau_params/peg_2khz.json

@@ -0,0 +1,12 @@
+{
+    "rotation_axis": "omega",
+    "scan_width_deg": 360.0,
+    "image_width_deg": 0.1,
+    "omega_start_deg": 0.0,
+    "exposure_time_s": 0.000475,
+    "acquire_time_s":  0.0005,
+    "rotation_direction": "NEGATIVE",
+    "shutter_opening_time_s": 0.6,
+    "storage_directory": "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning",
+    "nexus_filename": "glycerol"
+}

src/mx_bluesky/beamlines/i24/jungfrau_commissioning/callbacks/metadata_writer.py

@@ -70,8 +70,10 @@ def event(self, doc: dict):  # type: ignore
             self.flux_xbpm2 = data.get("beam_params_flux_xbpm2")
             self.flux_xbpm3 = data.get("beam_params_flux_xbpm3")
             self.wavelength = data.get("beam_params_wavelength")
+            self.energy_kev = data.get("beam_params_energy")
+            self.detector_distance = data.get("beam_params_det_distance")
             LOGGER.info(
-                f"Nexus handler received beam parameters, transmission: {self.transmission}, flux: {self.flux}, wavelength: {self.wavelength}."  # noqa
+                f"Nexus handler received beam parameters, transmission: {self.transmission}, flux: {self.flux}, wavelength: {self.wavelength}, det distance: {self.detector_distance}."  # noqa
             )
 
     def stop(self, doc: dict):  # type: ignore
@@ -92,6 +94,8 @@ def stop(self, doc: dict):  # type: ignore
                             "x": self.parameters.x_start_um,
                             "y": self.parameters.y_start_um,
                             "z": self.parameters.z_start_um,
+                            "detector_distance": self.detector_distance,
+                            "energy_kev": self.energy_kev,
                         }
                     )
                 )

src/mx_bluesky/beamlines/i24/jungfrau_commissioning/plans/gain_mode_darks_plans.py

@@ -8,12 +8,15 @@
     check_and_clear_errors,
     do_manual_acquisition,
     set_software_trigger,
+    wait_for_writing,
+    setup_detector
 )
 from mx_bluesky.beamlines.i24.jungfrau_commissioning.utils import run_number
 from mx_bluesky.beamlines.i24.jungfrau_commissioning.utils.jf_commissioning_devices import (
     JungfrauM1,
 )
 from mx_bluesky.beamlines.i24.jungfrau_commissioning.utils.log import LOGGER
+from mx_bluesky.beamlines.i24.jungfrau_commissioning.utils import i24
 
 
 class GainMode(str, Enum):
@@ -63,6 +66,8 @@ def do_darks(
     )
     os.makedirs(directory_prefix, exist_ok=True)
 
+    LOGGER.info(f"Writing data to {directory_prefix}")
+
     timeout_factor = max(10, timeout_factor * 0.001 / acq_time_s)
 
     # TODO CHECK IF FILES EXIST
@@ -105,3 +110,60 @@ def do_darks(
     yield from set_gain_mode(
         jungfrau, GainMode.dynamic, check_for_errors=check_for_errors
     )
+
+
+def do_pedestal_darks(    
+    jungfrau: JungfrauM1,
+    directory: str = "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning/",
+    check_for_errors=True,
+    exp_time_s=0.001,
+    acq_time_s=0.001,
+    focred_gain_ratio=10,
+    num_images=1000,
+    timeout_factor=6,
+    pedestal_frames=20,
+    pedestal_loops=200):
+
+    directory_prefix = (
+        Path(directory)
+        / f"{run_number(Path(directory)):05d}_darks_{acq_time_s}s_per_frame_pedestal"
+    )
+    os.makedirs(directory_prefix, exist_ok=True)
+
+    LOGGER.info(f"Writing data to {directory_prefix}")
+
+    yield from set_software_trigger(jungfrau)
+
+    yield from setup_detector(jungfrau, exp_time_s, acq_time_s, pedestal_frames*pedestal_loops*2)
+
+    yield from set_gain_mode(
+        jungfrau, GainMode.dynamic, check_for_errors=check_for_errors
+    )
+    yield from abs_set(jungfrau.file_directory, directory_prefix.as_posix(), wait=True)
+    yield from abs_set(jungfrau.file_name, "Pedestal", wait=True)
+
+    yield from abs_set(jungfrau.pedestal_frames, pedestal_frames, wait=True)
+    yield from abs_set(jungfrau.pedestal_loops, pedestal_loops, wait=True)
+
+    yield from abs_set(jungfrau.pedestal_mode, 1, wait=True)
+
+    yield from abs_set(jungfrau.acquire_start, 1, wait=True)
+    yield from wait_for_writing(jungfrau, 1000)
+
+
+    # yield from do_manual_acquisition(
+    #     jungfrau, exp_time_s, fg_acq_time, num_images, timeout_factor
+    # )
+
+    yield from sleep(0.3)
+
+    yield from abs_set(jungfrau.pedestal_mode, 0, wait=True)
+
+
+def take_darks():
+    """"Take darks in pedestal and old style, at 1kHz and 2kHz"""
+    jf = i24.jungfrau()
+    for time in [0.001, 0.0005]:
+        LOGGER.info(f"Taking data at exposure time = {time}")
+        yield from do_pedestal_darks(jf, exp_time_s=time, acq_time_s=time)
+        yield from do_darks(jf, exp_time_s=time, acq_time_s=time)

src/mx_bluesky/beamlines/i24/jungfrau_commissioning/plans/jungfrau_plans.py

@@ -9,6 +9,8 @@
     JungfrauM1,
     TriggerMode,
 )
+from mx_bluesky.beamlines.i24.jungfrau_commissioning.utils import run_number
+import os
 from mx_bluesky.beamlines.i24.jungfrau_commissioning.utils.log import LOGGER
 
 DIRECTORY = "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning/"
@@ -98,6 +100,33 @@ def do_manual_acq_with_new_filename(
     )
 
 
+def do_burst_mode(
+    jungfrau: JungfrauM1,
+    name: str,
+    exp_time_s: float,
+    acq_time_s: float,
+    n_frames: int,
+    directory: str = "/dls/i24/data/2024/cm37275-4/jungfrau_commissioning/",
+    timeout_times: float = 5,
+):
+    directory_prefix = (
+        Path(directory)
+        / f"{run_number(Path(directory)):05d}_burst_{n_frames}_frames_{acq_time_s}s_per_frame"
+    )
+    os.makedirs(directory_prefix, exist_ok=True)
+    LOGGER.info(
+        f"Using directory {directory_prefix.as_posix()}, setting directory and filename on detector..."
+    )
+    yield from bps.abs_set(jungfrau.file_name, name, wait=True)
+    yield from bps.abs_set(jungfrau.file_directory, directory_prefix.as_posix(), wait=True)
+    yield from bps.abs_set(jungfrau.burst_mode, 1)
+    yield from bps.sleep(0.2)
+    yield from do_manual_acquisition(
+        jungfrau, exp_time_s, acq_time_s, n_frames, timeout_times
+    )
+    yield from bps.abs_set(jungfrau.burst_mode, 0)
+
+
 def setup_detector(
     jungfrau: JungfrauM1,
     exposure_time_s: float,
@@ -118,11 +147,11 @@ def setup_detector(
         acquire_time_s,
         group=group,
     )
-    yield from bps.abs_set(
-        jungfrau.frame_count,
-        n_images,
-        group=group,
-    )
+    # yield from bps.abs_set(
+    #     jungfrau.frame_count,
+    #     n_images,
+    #     group=group,
+    # )
     if wait:
         yield from bps.wait(group)