Merge pull request #48 from DiamondLightSource/47_I24ssx_updates

Pull in latest updates

.gitignore

@@ -77,7 +77,8 @@ edm_serial/
 # Parameter files that could be modified by hand by scientists
 # or created during collection
 **/parameters/*.json
-**/parameters/fixed-target/*.txt
-**/parameters/fixed-target/cs/fiducials_*.txt
-**/parameters/fixed-target/*.json
-**/parameters/fixed-target/*/*.map
+**/parameters/*.txt
+**/parameters/fixed_target/*.txt
+**/parameters/fixed_target/cs/fiducial_*.txt
+**/parameters/fixed_target/*.json
+**/parameters/fixed_target/**/*.map

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=64", "setuptools_scm[toml]>=6.2", "wheel"]
+requires = ["setuptools>=64", "setuptools_scm[toml]==7.1.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]

src/mx_bluesky/I24/serial/extruder/i24ssx_Extruder_Collect_py3v2.py

@@ -7,6 +7,7 @@
 
 import argparse
 import logging
+import re
 import sys
 import time
 from datetime import datetime
@@ -113,9 +114,9 @@ def write_parameter_file(param_path: Path | str = PARAM_FILE_PATH):
 
     # If file name ends in a digit this causes processing/pilatus pain.
     # Append an underscore
-    numbers = ("0", "1", "2", "3", "4", "5", "6", "7", "8", "9")
     if det_type == "pilatus":
-        if filename.endswith(numbers):
+        m = re.search(r"\d+$", filename)
+        if m is not None:
             # Note for future reference. Appending underscore causes more hassle and
             # high probability of users accidentally overwriting data. Use a dash
             filename = filename + "-"
@@ -278,6 +279,23 @@ def run_extruderi24(args=None):
             sup.zebra1("quickshot", [gate_start, gate_width])
 
     elif det_type == "eiger":
+        logger.info("Using Eiger detector")
+
+        logger.warning(
+            """TEMPORARY HACK!
+            Running a Single image pilatus data collection to create directory."""
+        )  # See https://github.com/DiamondLightSource/mx_bluesky/issues/45
+        num_shots = 1
+        sup.pilatus("quickshot-internaltrig", [filepath, filename, num_shots, exp_time])
+        logger.debug("Sleep 2s waiting for pilatus to arm")
+        sleep(2.5)
+        caput(pv.pilat_acquire, "0")  # Disarm pilatus
+        sleep(0.5)
+        caput(pv.pilat_acquire, "1")  # Arm pilatus
+        logger.debug("Pilatus data collection DONE")
+        sup.pilatus("return to normal")
+        logger.info("Pilatus back to normal. Single image pilatus data collection DONE")
+
         caput(pv.eiger_seqID, int(caget(pv.eiger_seqID)) + 1)
         logger.info("Eiger quickshot setup: filepath %s" % filepath)
         logger.info("Eiger quickshot setup: filepath %s" % filename)

src/mx_bluesky/I24/serial/fixed_target/FT-gui-edm/DiamondChipI24-py3v1.edl

@@ -2125,7 +2125,7 @@ offColor index 16
 topShadowColor index 7
 botShadowColor index 7
 controlPv "ME14E-MO-CHIP-01:PMAC_STRING"
-pressValue "#2J:-10"
+pressValue "#2J:10"
 releaseValue "#2P"
 3d
 font "helvetica-medium-r-18.0"
@@ -2237,7 +2237,7 @@ offColor index 16
 topShadowColor index 7
 botShadowColor index 7
 controlPv "ME14E-MO-CHIP-01:PMAC_STRING"
-pressValue "#2J:-60"
+pressValue "#2J:60"
 releaseValue "#2P"
 offLabel "-3"
 3d
@@ -2260,7 +2260,7 @@ offColor index 16
 topShadowColor index 7
 botShadowColor index 7
 controlPv "ME14E-MO-CHIP-01:PMAC_STRING"
-pressValue "#2J:60"
+pressValue "#2J:-60"
 releaseValue "#2P"
 offLabel "+3"
 3d
@@ -2283,7 +2283,7 @@ offColor index 16
 topShadowColor index 7
 botShadowColor index 7
 controlPv "ME14E-MO-CHIP-01:PMAC_STRING"
-pressValue "#2J:10"
+pressValue "#2J:-10"
 releaseValue "#2P"
 3d
 font "helvetica-medium-r-18.0"
@@ -2305,7 +2305,7 @@ offColor index 19
 topShadowColor index 7
 botShadowColor index 7
 controlPv "ME14E-MO-CHIP-01:PMAC_STRING"
-pressValue "#2J:31750"
+pressValue "#2J:-31750"
 releaseValue "#2P"
 onLabel "Y+Y"
 offLabel "+Y+"
@@ -2377,7 +2377,7 @@ offColor index 19
 topShadowColor index 7
 botShadowColor index 7
 controlPv "ME14E-MO-CHIP-01:PMAC_STRING"
-pressValue "#2J:-31750"
+pressValue "#2J:31750"
 releaseValue "#2P"
 onLabel "Y-Y"
 offLabel "-Y-"
@@ -2493,7 +2493,7 @@ offColor index 17
 topShadowColor index 7
 botShadowColor index 7
 controlPv "ME14E-MO-CHIP-01:PMAC_STRING"
-pressValue "#2J:-3750"
+pressValue "#2J:3750"
 releaseValue "#2P"
 offLabel "-3"
 3d
@@ -2516,7 +2516,7 @@ offColor index 17
 topShadowColor index 7
 botShadowColor index 7
 controlPv "ME14E-MO-CHIP-01:PMAC_STRING"
-pressValue "#2J:-1250"
+pressValue "#2J:1250"
 releaseValue "#2P"
 offLabel "-1"
 3d
@@ -2539,7 +2539,7 @@ offColor index 17
 topShadowColor index 7
 botShadowColor index 7
 controlPv "ME14E-MO-CHIP-01:PMAC_STRING"
-pressValue "#2J:3750"
+pressValue "#2J:-3750"
 releaseValue "#2P"
 offLabel "+3"
 3d
@@ -2562,7 +2562,7 @@ offColor index 17
 topShadowColor index 7
 botShadowColor index 7
 controlPv "ME14E-MO-CHIP-01:PMAC_STRING"
-pressValue "#2J:1250"
+pressValue "#2J:-1250"
 releaseValue "#2P"
 offLabel "+1"
 3d

src/mx_bluesky/I24/serial/fixed_target/i24ssx_Chip_Manager_py3v1.py

@@ -7,6 +7,7 @@
 import argparse
 import json
 import logging
+import re
 import shutil
 import sys
 import time
@@ -125,16 +126,20 @@ def write_parameter_file(param_path: Path | str = PARAM_FILE_PATH_FT):
     map_type = caget(pv.me14e_gp2)
     chip_type = caget(pv.me14e_gp1)
     det_type = caget(pv.me14e_gp101)
+
+    # If file name ends in a digit this causes processing/pilatus pain.
+    # Append an underscore
     if det_type == "pilatus":
         caput(pv.pilat_cbftemplate, 0)
-        numbers = ("0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10")
-        if filename.endswith(numbers):
+        m = re.search(r"\d+$", filename)
+        if m is not None:
             # Note for future reference. Appending underscore causes more hassle and
             # high probability of users accidentally overwriting data. Use a dash
             filename = filename + "-"
-            logger.warning(
+            logger.info(
                 "Requested filename ends in a number. Appended dash: %s" % filename
             )
+
     # historical - use chip_name instead of filename
     chip_name = filename
 
@@ -744,7 +749,7 @@ def fiducial(point: int = 1, param_path: Path | str = CS_FILES_PATH):
     logger.info("MTR\tRBV\tRAW\tCorr\tf_value")
     logger.info("MTR1\t%1.4f\t%i\t%i\t%1.4f" % (rbv_1, raw_1, mtr1_dir, f_x))
     logger.info("MTR2\t%1.4f\t%i\t%i\t%1.4f" % (rbv_2, raw_2, mtr2_dir, f_y))
-    logger.info("MTR3\t%1.4f\t%i\t%i\t%1.4f" % (rbv_3, raw_3, mtr3_dir, f_y))
+    logger.info("MTR3\t%1.4f\t%i\t%i\t%1.4f" % (rbv_3, raw_3, mtr3_dir, f_z))
 
     with open(param_path / f"fiducial_{point}.txt", "w") as f:
         f.write("MTR\tRBV\tRAW\tCorr\tf_value\n")
@@ -955,11 +960,17 @@ def pumpprobe_calc():
     repeat3 = 6 * 20 * (movetime + (pumpexptime + exptime) / 2)
     repeat5 = 10 * 20 * (movetime + (pumpexptime + exptime) / 2)
     repeat10 = 20 * 20 * (movetime + (pumpexptime + exptime) / 2)
-    logger.info("repeat1 (%s): %s s" % (pv.me14e_gp104, round(repeat1, 4)))
-    logger.info("repeat2 (%s): %s s" % (pv.me14e_gp105, round(repeat2, 4)))
-    logger.info("repeat3 (%s): %s s" % (pv.me14e_gp106, round(repeat3, 4)))
-    logger.info("repeat5 (%s): %s s" % (pv.me14e_gp107, round(repeat5, 4)))
-    logger.info("repeat10 (%s): %s s" % (pv.me14e_gp108, round(repeat10, 4)))
+    for pv_name, repeat in (
+        (pv.me14e_gp104, repeat1),
+        (pv.me14e_gp105, repeat2),
+        (pv.me14e_gp106, repeat3),
+        (pv.me14e_gp107, repeat5),
+        (pv.me14e_gp108, repeat10),
+    ):
+        rounded = round(repeat, 4)
+        caput(pv_name, rounded)
+        logger.info("Repeat (%s): %s s" % (pv_name, rounded))
+    # logger.info("repeat10 (%s): %s s" % (pv.me14e_gp108, round(repeat10, 4)))
     logger.debug("PP calculations done")
 
 

src/mx_bluesky/I24/serial/parameters/fixed_target/cs/fiducial_1.txt

@@ -1,4 +1,4 @@
 MTR	RBV	RAW	Corr	f_value
-MTR1	25.3970	254270	1	25.3970
-MTR2	-0.3604	3608	-1	-0.3604
+MTR1	25.3946	254246	1	25.3946
+MTR2	-0.3833	3838	-1	-0.3833
 MTR3	0.0000	0	-1	0.0000

src/mx_bluesky/I24/serial/parameters/fixed_target/cs/fiducial_2.txt

@@ -1,4 +1,4 @@
 MTR	RBV	RAW	Corr	f_value
-MTR1	0.3718	3722	1	0.3718
-MTR2	25.3952	-254255	-1	25.3952
+MTR1	0.3941	3946	1	0.3941
+MTR2	25.3958	-254261	-1	25.3958
 MTR3	0.0000	0	-1	0.0000

src/mx_bluesky/I24/serial/parameters/fixed_target/parameters.txt

@@ -1,13 +1,13 @@
 visit 		/dls/i24/data/2023/cm33852-4/
-chip_name 	beta
-protein_name 	test2_20230912/test2
+chip_name 	albion
+protein_name 	test_20230919/eigertest3
 n_exposures 	1
 chip_type 	0
 map_type 	1
 pump_repeat 	0
 pumpexptime 	0
 pumpdelay 	0
 prepumpexptime 	0
-exptime 	0.005
-dcdetdist 	1300
-det_type 	pilatus
+exptime 	0.01
+dcdetdist 	1480
+det_type 	eiger

src/mx_bluesky/I24/serial/setup_beamline/pv_abstract.py

@@ -22,8 +22,8 @@ class Pilatus:
         round(a * b, 3) for a, b in zip(image_size_pixels, pixel_size_mm)
     )
 
-    det_y_threshold = 50.0
-    det_y_target = 0.0
+    det_y_threshold = 560.0
+    det_y_target = 566.0
 
     class pv:
         detector_distance = pv.pilat_detdist
@@ -48,8 +48,8 @@ class Eiger:
         round(a * b, 3) for a, b in zip(image_size_pixels, pixel_size_mm)
     )
 
-    det_y_threshold = 200.0
-    det_y_target = 220.0
+    det_y_threshold = -10.0
+    det_y_target = -22.0
 
     class pv:
         detector_distance = pv.eiger_detdist

src/mx_bluesky/I24/serial/setup_beamline/setup_beamline.py

@@ -14,7 +14,7 @@ class UnknownDetectorType(Exception):
 
 def get_detector_type() -> Detector:
     det_y = caget(pv.det_y)
-    if float(det_y) > Eiger.det_y_threshold:
+    if float(det_y) < Eiger.det_y_threshold:
         logger.info("Eiger detector in use.")
         return Eiger()
     elif float(det_y) > Pilatus.det_y_threshold:

src/mx_bluesky/I24/serial/write_nexus.py

@@ -12,13 +12,13 @@ def call_nexgen(
     chip_prog_dict,
     start_time,
     param_file_tuple,
-    expt_type="fixed_target",
+    expt_type="fixed-target",
     total_numb_imgs=None,
 ):
     det_type = str(caget(pv.me14e_gp101))
     print(f"det_type: {det_type}")
 
-    if expt_type == "fixed_target":
+    if expt_type == "fixed-target":
         (
             chip_name,
             visit,

tests/I24/serial/extruder/test_extruder_collect.py

@@ -97,6 +97,11 @@ def test_moveto_laseroff_for_pilatus(fake_caget, fake_caput, dummy_parser):
 @patch("mx_bluesky.I24.serial.extruder.i24ssx_Extruder_Collect_py3v2.caput")
 @patch("mx_bluesky.I24.serial.extruder.i24ssx_Extruder_Collect_py3v2.caget")
 @patch("mx_bluesky.I24.serial.extruder.i24ssx_Extruder_Collect_py3v2.sup")
-def test_run_extruder(fake_sup, fake_caget, fake_caput, fake_nexgen, fake_dcid):
+def test_run_extruder_with_eiger(
+    fake_sup, fake_caget, fake_caput, fake_nexgen, fake_dcid
+):
     run_extruderi24()
     assert fake_nexgen.call_count == 1
+    assert fake_dcid.call_count == 1
+    # Check temporary piilatus hack is in there
+    assert fake_sup.pilatus.call_count == 2

tests/I24/serial/fixed-target/test_chip_manager.py

@@ -1,5 +1,5 @@
 import json
-from unittest.mock import MagicMock, mock_open, patch
+from unittest.mock import ANY, MagicMock, call, mock_open, patch
 
 import pytest
 
@@ -8,6 +8,7 @@
     cs_reset,
     moveto,
     parse_args_and_run_parsed_function,
+    pumpprobe_calc,
     scrape_mtr_directions,
     scrape_mtr_fiducials,
 )
@@ -168,3 +169,21 @@ def test_arg_parser_runs_define_current_chip_function_as_expected(
 ):
     parse_args_and_run_parsed_function(["define_current_chip", "chip_id"])
     mock_define_current_chip.assert_called_once_with("chip_id")
+
+
+@patch("mx_bluesky.I24.serial.fixed_target.i24ssx_Chip_Manager_py3v1.caput")
+@patch("mx_bluesky.I24.serial.fixed_target.i24ssx_Chip_Manager_py3v1.caget")
+def test_pumpprobe_calc(fake_caget, fake_caput):
+    fake_caget.side_effect = [0.01, 0.005]
+    pumpprobe_calc()
+    assert fake_caget.call_count == 2
+    assert fake_caput.call_count == 5
+    fake_caput.assert_has_calls(
+        [
+            call(ANY, 0.62),
+            call(ANY, 1.24),
+            call(ANY, 1.86),
+            call(ANY, 3.1),
+            call(ANY, 6.2),
+        ]
+    )

tests/I24/serial/setup_beamline/test_setup_beamline.py

@@ -7,10 +7,16 @@
 
 @patch("mx_bluesky.I24.serial.setup_beamline.setup_beamline.caget")
 def test_get_detector_type(fake_caget):
-    fake_caget.return_value = 205
+    fake_caget.return_value = -22
     assert setup_beamline.get_detector_type().name == "eiger"
 
 
+@patch("mx_bluesky.I24.serial.setup_beamline.setup_beamline.caget")
+def test_get_detector_type_finds_pilatus(fake_caget):
+    fake_caget.return_value = 566
+    assert setup_beamline.get_detector_type().name == "pilatus"
+
+
 @patch("mx_bluesky.I24.serial.setup_beamline.setup_beamline.caput")
 def test_beamline_collect(fake_caput):
     setup_beamline.beamline("collect")