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Bug fixes after testing recent changes
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@rhfogh
rhfogh committed Dec 4, 2024
1 parent a2cbc84 commit b758690
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Showing 4 changed files with 129 additions and 132 deletions.
12 changes: 5 additions & 7 deletions mxcubecore/HardwareObjects/Gphl/GphlWorkflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@ class GphlWorkflowStates(enum.Enum):
"4mxt":{
"exposureTime": 0.055,
"oscillationRange": 0.15,
"radiationSensitivity": 1.0,
"radiationSensitivity": 1.3,
"energy": 12.2222,
},
}
Expand Down Expand Up @@ -676,6 +676,7 @@ def query_pre_strategy_params(self, choose_lattice=None):
):
fields[tag]["readOnly"] = False
ui_schema["parameters"]["column1"]["ui:order"].remove("point_groups")
fields["crystal_thickness"]["readOnly"] = False

elif not choose_lattice:
# Characterisation
Expand Down Expand Up @@ -1112,10 +1113,7 @@ def query_collection_strategy(self, geometric_strategy):

# set starting and unchanging values of parameters
resolution = HWR.beamline.resolution.get_value()
dose_budget = self.resolution2dose_budget(
resolution,
decay_limit=data_model.decay_limit,
)
dose_budget = data_model.recommended_dose_budget(resolution)
# NB These default values are set just before this function is called
default_image_width = data_model.image_width
default_exposure = data_model.exposure_time
Expand Down Expand Up @@ -2701,10 +2699,10 @@ def maximum_dose_rate(energy=None):
def rotation_axis_index(self):
"""Get index of rotation axis
Rotation axis is assumed to be witehr X or Y
Rotation axis is assumed to be either X or Y
"""
coords = list(abs(val) for val in list(self.rotation_axes.values())[0])
if coords[0] < coords[1]:
if coords[0] > coords[1]:
return 0
else:
return 1
Expand Down
226 changes: 115 additions & 111 deletions mxcubecore/configuration/mockup/gphl/gphl-workflow.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -99,44 +99,48 @@ settings:
# (which may override this value)
# Any other true value reads from auto_acq_parameters below
# automation_mode: TEST_FROM_FILE
# automation_mode: MASSIF1

# Default parameters for fully automated strategies
# Multiple acquisitions in order - characterisation then main
# passed to set_pre_strategy_params and set_pre_acquisition_params
# NB as long as we only acquire either characterisation+main or diffractcal
# the code will use list[0] for the first acquisition
# and list[-1] for the main one
auto_acq_parameters:
# For characterisation acquisition
- exposure_time: 0.02
image_width: 0.1
# resolution: 1.928
strategy: Char_4_by_10_multitrigger
# init_spot_dir: /directory/containing/SPOT.XDS/file/after/characterisation
# strategy_options: # Not currently used
# For acquisition or diffractcal
# Expectation for crystal classes - needed for indexing selection.
# Default parameters for fully automated strategies
# Multiple acquisitions in order - characterisation then main
# passed to set_pre_strategy_params and set_pre_acquisition_params
# NB as long as we only acquire either characterisation+main or diffractcal
# the code will use list[0] for the first acquisition
# and list[-1] for the main one
auto_acq_parameters:
# For characterisation acquisition
- exposure_time: 0.02
image_width: 0.1
# resolution: 1.928
strategy: Char_6_5_multitrigger
# init_spot_dir: /directory/containing/SPOT.XDS/file/after/characterisation
# strategy_options: # Not currently used
# For acquisition or diffractcal
# Expectation for crystal classes - needed for indexing selection.

# crystal_classes:
# - 222P
# - 222C
# - 222I
# space_group: I222
- exposure_time: 0.02
image_width: 1.0
resolution: 1.5
snapshot_count: 2
wedge_width: 15.0
strategy: full
repetition_count: 1
# strategy_options:
# # Program options passed directly to stratcal - not needed normally
# Override default settings
# angular_tolerance, maximum_chi, and clip_kappa are defined in
# settings (above) and strategy_type and variant by program
# maximum_chi: 48.0
# angular_tolerance: 1.0
# option_name: 999.999
# crystal_classes:
# - 222P
# - 222C
# - 222I
# space_group: I222
- exposure_time: 0.02
image_width: 1.0
resolution: 1.5
snapshot_count: 2
wedge_width: 15.0
strategy: full
repetition_count: 1
# energies:
# - 12.111
# - 12.222
# strategy_options:
# # Program options passed directly to stratcal - not needed normally
# Override default settings
# angular_tolerance, maximum_chi, and clip_kappa are defined in
# settings (above) and strategy_type and variant by program
# maximum_chi: 48.0
# angular_tolerance: 1.0
# option_name: 999.999

# Java invocation properties - syntax is e.g. '-Dfile.encoding=UTF-8'
invocation_properties:
Expand Down Expand Up @@ -316,80 +320,80 @@ workflows:
# File name pattern for characterisation data collection
charpattern: generic

"GΦL Diffractometer calibration":
wfpath: Gphl
wftype: diffractcal
requires:
- point
options:
# NB you must set EITHER wfprefix OR samplesubdir (or both)
# wfprefix is the enactment fixed file prefix
# wfprefix: gphl_wf_
# Include sample filename prefix as subdirextory in enactment directory path
# Any
samplesubdir: null
# # directory paths are:
# wfprefix: .../RAW_DATA/<wfprefix>_001/...
# samplesubdir: .../RAW_DATA/<filenameprefix>_001/...
# both: .../RAW_DATA/<filenameprefix>/<wfprefix>_001/...
"GΦL Diffractometer calibration":
wfpath: Gphl
wftype: diffractcal
requires:
- point
options:
# NB you must set EITHER wfprefix OR samplesubdir (or both)
# wfprefix is the enactment fixed file prefix
# wfprefix: gphl_wf_
# Include sample filename prefix as subdirextory in enactment directory path
# Any
samplesubdir: null
# # directory paths are:
# wfprefix: .../RAW_DATA/<wfprefix>_001/...
# samplesubdir: .../RAW_DATA/<filenameprefix>_001/...
# both: .../RAW_DATA/<filenameprefix>/<wfprefix>_001/...

strategies:
- title: Diffractometer calibration
strategy_type: diffractcal
wf_selection: diffractcal
variants:
- full
- short
documentation: |
Diffractometer calibration.
Designed for use by beamline personnel.
Calibrates axis directions, detector pane orientation,
and beam centre.
Long data collection and processing, requiring a high-quality,
high-symmetry crystal of precisely known cell parameters.
Variants:
full: 22 60-deg sweeps, 11 orientations
short: 6 60-deg sweeps, 3 orientations
options:
# wfprefix: Dcalib2_
# Name of strategy from library to use. Variant name is appended
strategy: DiffractCal_
# File name for diffractometer calibration output
calibration: diffractcal
# Pattern name for characterisation collections, used for all data
charpattern: multiorientation
# copy calibration result to configuration directory,
# moving aside previous value
# updateblconfig: null
# # Path of file to dump persisted instrumentation configuration. OPTIONAL
# instcfgout: gphl_diffractcal_out.nml
strategies:
- title: Diffractometer calibration
strategy_type: diffractcal
wf_selection: diffractcal
variants:
- full
- short
documentation: |
Diffractometer calibration.
Designed for use by beamline personnel.
Calibrates axis directions, detector pane orientation,
and beam centre.
Long data collection and processing, requiring a high-quality,
high-symmetry crystal of precisely known cell parameters.
Variants:
full: 22 60-deg sweeps, 11 orientations
short: 6 60-deg sweeps, 3 orientations
options:
# wfprefix: Dcalib2_
# Name of strategy from library to use. Variant name is appended
strategy: DiffractCal_
# File name for diffractometer calibration output
calibration: diffractcal
# Pattern name for characterisation collections, used for all data
charpattern: multiorientation
# copy calibration result to configuration directory,
# moving aside previous value
# updateblconfig: null
# # Path of file to dump persisted instrumentation configuration. OPTIONAL
# instcfgout: gphl_diffractcal_out.nml

"GΦL Translational Calibration":
wfpath: Gphl
wftype: transcal
requires:
- samplegrid
strategies:
- title: Translational Calibration
strategy_type: transcal
wf_selection: transcal
variants:
- full
documentation: |
Translational calibration.
Designed for use by beamline personnel.
Calibrates centring motors to allow prediction of centring positions
Consists of mulltiple centrings, requiring a glass or tungsten tip
options:
# file: File containing settings of rotation axes for calibration
# The name is the relative path from the gphl_beamline_config directory
# grid: Grid definition [axis_name:start:end:step],
# slowest-varying to fastest varying
# EITHER file OR grid must be set.-->
# grid: grid_axes_spec
file: transcal_2stage.json
# copy calibration result to configuration directory,
# renaming previous result file
updateblconfig: null
# Path of file to dump persisted instrumentation configuration. OPTIONAL
# instcfgout: gphl_transcal_out.nml
"GΦL Translational Calibration":
wfpath: Gphl
wftype: transcal
requires:
- samplegrid
strategies:
- title: Translational Calibration
strategy_type: transcal
wf_selection: transcal
variants:
- full
documentation: |
Translational calibration.
Designed for use by beamline personnel.
Calibrates centring motors to allow prediction of centring positions
Consists of mulltiple centrings, requiring a glass or tungsten tip
options:
# file: File containing settings of rotation axes for calibration
# The name is the relative path from the gphl_beamline_config directory
# grid: Grid definition [axis_name:start:end:step],
# slowest-varying to fastest varying
# EITHER file OR grid must be set.-->
# grid: grid_axes_spec
file: transcal_2stage.json
# copy calibration result to configuration directory,
# renaming previous result file
updateblconfig: null
# Path of file to dump persisted instrumentation configuration. OPTIONAL
# instcfgout: gphl_transcal_out.nml
2 changes: 1 addition & 1 deletion mxcubecore/configuration/mockup/lims-client-mockup.xml
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
<object class="ISPyBClientMockup">
<loginType>user</loginType>
</object>
</object>
21 changes: 8 additions & 13 deletions mxcubecore/model/queue_model_objects.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2287,11 +2287,11 @@ def set_pre_acquisition_params(
self.snapshot_count = int(snapshot_count)
if recentring_mode:
self.recentring_mode = recentring_mode
energy_tags = (settings["default_beam_energy_tag"],)
if self.characterisation_done:
energy_tags = self.strategy_settings.get("beam_energy_tags", energy_tags)
if energies:
# Energies are *added* to existing list
energy_tags = self.strategy_settings.get(
"beam_energy_tags", (settings["default_beam_energy_tag"],)
)
wavelengths = list(self.wavelengths)
offset = len(wavelengths)
if len(energies) == len(energy_tags) - offset:
Expand All @@ -2304,16 +2304,11 @@ def set_pre_acquisition_params(
)
)
self.wavelengths = tuple(wavelengths)
elif not (
len(energies) == len(energy_tags)
and len(energies) == len(wavelengths)
and self.automation_mode
):
# In automation mode energies and wavelengths are set together earlier
raise ValueError(
"Number of energies %s do not match remaining slots %s"
% (energies, energy_tags[len(self.wavelengths) :])
)
if len(self.wavelengths) != len(energy_tags):
raise ValueError(
"Number of energies: %s do not match slots %s"
% (len(self.wavelengths), energy_tags)
)
if skip_collection:
self.skip_collection = True

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