diff --git a/examples/data/stm/output.nxs b/examples/data/stm/output.nxs
deleted file mode 100644
index ea12f3891a79585b6b296017501f8a087f9a6573..0000000000000000000000000000000000000000
Binary files a/examples/data/stm/output.nxs and /dev/null differ
diff --git a/examples/data/stm/stm.zip b/examples/data/stm/stm.zip
deleted file mode 100644
index a04e9e8107c4bf957fbffa5cbc74075dde80455c..0000000000000000000000000000000000000000
Binary files a/examples/data/stm/stm.zip and /dev/null differ
diff --git a/examples/data/stm/stm_example.archive.json b/examples/data/stm/stm_example.archive.json
deleted file mode 100644
index 35766f5aa7a2f2c199be965b8e0f81648e115344..0000000000000000000000000000000000000000
--- a/examples/data/stm/stm_example.archive.json
+++ /dev/null
@@ -1 +0,0 @@
-{"data":{"m_def":"../upload/raw/STS.scheme.archive.yaml#/definitions/section_definitions/0","reader":"stm","nxdl":"NXsts","input_files":["config_file_for_sxm.json","STM_nanonis_generic_5e.sxm","eln_data.yaml"],"definition":"NXsts","experiment_type":"stm","type":"background","collection_identifier":"TiSe2_2303a_annealing_300C_5min_evaporate_Pyrene_1_","Instrument":{"software":{"version":"Generic 5e","vendor":"nanonis","rt_release":"10771","ui_release":"10771"},"lock_in":{"lock_in_data_flip_number":-1,"status":"OFF","modulation_frequency":973,"modulation_amplitude":0.005},"hardware":{"name":"Nanonis"},"stm_head_temp":5.04866,"sample_bias":{"bias":0.005,"bias_calibration":1,"bias_offset":"0"},"piezo_config":{"active_calib":"LHe"}},"experiment_identifier":"C:\\Users\\SPM-PEEM\\Desktop\\DATA_Nanonis\\20220711_CreaTec_Service_Benchmarks_LHe\\Nanonis-Session-PMD100-HVHU_CreaTec_Service_PalmaLabBerlin220711","experiment_description":"A new TiSe2, annealed at 300 C for 5 min, then cool down to RT, evaporate the Pyrene on RT, 2.2 E -7, totally 10 s.","entry_identifier":"TiSe2_2303a_annealing_300C_5min_evaporate_Pyrene_1_0070"}}
\ No newline at end of file
diff --git a/examples/data/sts/STS.scheme.archive.yaml b/examples/data/sts/STS.scheme.archive.yaml
deleted file mode 100644
index 2878fd5942d396f18759b5d566acd91e5fb0df76..0000000000000000000000000000000000000000
--- a/examples/data/sts/STS.scheme.archive.yaml
+++ /dev/null
@@ -1,655 +0,0 @@
-definitions:
- name: Eln example for NXiv_sweep2
- sections:
- stm:
- base_sections:
- - nomad.datamodel.metainfo.eln.NexusDataConverter
- - nomad.datamodel.data.EntryData
- m_annotations:
- template:
- reader: sts
- nxdl: NXsts
- eln:
- hide: []
- quantities:
- definition:
- type:
- type_kind: Enum
- type_data:
- - NXsts
- m_annotations:
- eln:
- component: EnumEditQuantity
- description: ''
- experiment_type:
- type:
- type_kind: Enum
- type_data:
- - sts
- - stm
- m_annotations:
- eln:
- component: EnumEditQuantity
- description: 'Only two type of experiments are allowed: sts and stm.'
- type:
- type:
- type_kind: Enum
- type_data:
- - background
- - reference
- - sample
- # TODO: Are there other types e.g. foreground
- m_annotations:
- eln:
- component: EnumEditQuantity
- description: |
- The equipments and techniques as well as the parameter settings
- and reference signals are used during the experiments used in the scanning
- tunneling microscopy(STM).
- entry_identifier:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- description: |
- The name of the output file, with the number of scans at the end.e.g.
- (e.g. 221122_Au_5K00014) '
- # TODO: Confirm it.
- collection_identifier:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- description: |
- The name of the series output file, which represents only
- the public part of the output file. (e.g. 221122_Au_5K).
- experiment_identifier:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- description: |
- Path to storage of output files. (e.g. Path C:\Users\SPM-PEEM\Desktop\DATA_Nanonis\20220711_CreaTec_Service_Benchmarks_LHe\Nanonis-Session-PMD100-HVHU_CreaTec_Service_PalmaLabBerlin220711)
- experiment_description:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- description: |
- Descriptive comments for this experiment, added by the experimenter,
- coming from the output file. (e.g. Comment01 SYNC & Filter LP 8order WITHDRAW
- 600 steps, locked Au(111), 50pA, 100 mV set point, 1mV DCA, 973Hz,138
- 1st H, -84 2nd H).
- sub_sections:
- Instrument:
- section:
- m_annotations:
- eln:
- overview: true
- sub_sections:
- hardware:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- name:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- description: |
- Name of the hardware. (e.g. Nanonis BP5e).
- software:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- version:
- type:
- type_kind: Enum
- type_data:
- - Generic 5e
- m_annotations:
- eln:
- component: EnumEditQuantity
- description: Version of the software.
- vendor:
- type:
- type_kind: Enum
- type_data:
- - nanonis
- m_annotations:
- eln:
- component: EnumEditQuantity
- description: Vendor of the software.
- rt_release:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- description: RT release.
- ui_release:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- description: UI release.
- current_amplifier:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- amplification_factor:
- type: np.float64
- m_annotations:
- eln:
- component: NumberEditQuantity
- description: |
- The amplification factor of the current amplifier. (e.g. 1E+3).
- lock_in:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- status:
- type:
- type_kind: Enum
- type_data:
- - "ON"
- - "OFF"
- m_annotations:
- eln:
- component: EnumEditQuantity
- description: |
- Status of Lock-in device whether while ferfoming the experiment.
- modulation_signal:
- type: np.float64
- unit: V
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: V
- description: |
- This is the signal on which the modulation (sine) will be added.
- modulation_frequency:
- type: np.float64
- unit: Hz
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: Hz
- description: |
- The signal is modulated by adding the frequency of the sine modulation. The
- modulation frequency spans can be from 10 mHz to 40 kHz, corresponding to the output filter
- cut-off range. When dealing with harmonics, it's essential to ensure that the
- harmonic frequencies remain below ~100 kHz, which aligns with the input filter cut-off.
- Be mindful that hardware filters might impact the amplitude as the signal approaches
- their cut-off frequencies (e.g. 973E+0).
- modulation_amplitude:
- type: np.float64
- unit: V
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: V
- description: |
- The amplitude (in physical units of modulated signal) of the sine modulation.
- demodulated_signal:
- type: np.float64
- unit: A
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: A
- description: |
- The input signal (STS signal) will be demodulated, in order to
- determine the amplitude and phase at the frequency set in the
- Frequency field or harmonics, such as current, bias, et.al.
- lock_in_data_flip_number:
- type: np.float64
- m_annotations:
- eln:
- component: NumberEditQuantity
- description: |
- Whether to flip the surve or not.
- sample_bias:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- bias:
- type: np.float64
- unit: V
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: V
- description: Applied a voltage between tip and sample.
- bias_calibration:
- type: np.float64
- m_annotations:
- eln:
- component: NumberEditQuantity
- bias_offset:
- type: str
- unit: V
- m_annotations:
- eln:
- component: StringEditQuantity
- defaultDisplayUnit: V
- description: ''
- piezo_config:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- active_calib:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- description: |
- The name of caliberation type. (e.g. LHe).
- drift_correction_status:
- type: bool
- m_annotations:
- eln:
- component: BoolEditQuantity
- defaultDisplayUnit: on/off
- description: |
- Use the button to turn on/off the drift compensation. (e.g. FALSE).
- Environment:
- section:
- m_annotations:
- eln:
- overview: true
- sub_sections:
- Current_sensor:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- current:
- type: np.float64
- unit: A
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: A
- description: ' This is set-point of tip current. '
- current_calibration:
- type: np.float64
- unit: A/V
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: A/V
- description: Value of calibration that comes as A/V.
- current_offset:
- type: np.float64
- unit: A
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: A
- description: ''
- current_gain:
- type: np.float64
- m_annotations:
- eln:
- component: NumberEditQuantity
- Position:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- x:
- type: np.float64
- unit: m
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: m
- description: |
- The scanning area in x position in the frame. (e.g. -890.53E-12) '
- y:
- type: np.float64
- unit: m
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: m
- description: |
- The scanning area in y position in the frame. (e.g. 29.6968E-9) '
- z:
- type: np.float64
- unit: m
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: m
- description: |
- The scanning area in x position in the frame. (e.g. 130.5E-9).
- sub_sections:
- z_controller:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- z:
- type: np.float64
- unit: m
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: m
- description: |
- Indicate the tip position Z between tip and sample. The tip
- position can also be varied when the controller is not
- running. (e.g. 130.5E-9).
- Sweep_control:
- section:
- m_annotations:
- eln:
- overview: true
- sub_sections:
- Bias_spectroscopy:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- integration_time:
- type: np.float64
- unit: s
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: s
- description: |
- Time during which the spectroscopy data are acquired and
- averaged. (e.g. 150E-6).
- number_of_sweeps:
- type: np.float64
- m_annotations:
- eln:
- component: NumberEditQuantity
- description:
- Number of sweeps to measure and average. (e.g. 100).
- sweep_start:
- type: np.float64
- unit: V
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: V
- description: |
- The first bias values of the sweep. (e.g. -300E-3) '
- sweep_end:
- type: np.float64
- unit: V
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: V
- description: |
- The last bias values of the sweep (e.g. 300E-3).
- num_pixel:
- type: np.float64
- m_annotations:
- eln:
- component: NumberEditQuantity
- description: |
- Define the sweep number of points, that is, the maximum
- spectrum resolution eq. Bias window divide by Num Pixel
- (e.g. 4096).
- z_avg_time:
- type: np.float64
- unit: s
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: s
- description: |
- Duration over which the Z position is recorded and averaged
- before and after the sweep (the latter only if Record final Z
- position is selected in the Advanced section). After the
- initial Z averaging time, if Z-Controller to Hold is selected
- in the Advanced section, the Z-Controller is set to hold and
- the tip is placed at the previously averaged Z position (plus
- Z offset). (e.g. 100E-3).
- circuit:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- rt_frequency:
- type: np.float64
- unit: Hz
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: Hz
- description: |
- The bandwitdh of the Hardware and/or Software which is
- insturment specific. For example: Nanonis Generic 5 has RT
- Frequency 20E-3.
- signals_oversampling:
- type: np.float64
- m_annotations:
- eln:
- component: NumberEditQuantity
- description: |
- (Signals Periods) The Signals Period is the rate at which
- the signals are transferred to the host computer running the
- control software. This is usually lower by a factor of 10
- than the sampling rate, because an internal oversampling of the
- signal is done on the real time engine. You can reduce the
- oversampling down to 1 in order to resolve higher frequencies
- in the Spectrum Analyzer. (e.g. 10).
- acquisition_period:
- type: np.float64
- unit: s
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: s
- description: |
- Update rate for several processes like History Graph,
- Auto-Approach, and for many Programming Interface functions.
- This is usually set to 20 ms. All additional timings (7-9)
- can only be integer multiples of this value. They can be set
- to different values, but the actual timing value will be
- coerced to a multiple of the Acquisition Period. (e.g. 20E-3).
- animations_period:
- type: np.float64
- unit: s
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: s
- description: |
- Update rate of animated graphical indicators. These are e.g.
- some graphs & sliders. A reasonable value is 40 ms (25 updates
- per second). Increase this period to reduce the processor load
- for the graphical user interface, especially on slow computers.
- This value is purely a user interface update rate and does not
- affect measurements in any way. (e.g. 20E-3) '
- indicators_period:
- type: np.float64
- unit: s
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: s
- description: |
- Update rate of digital indicators, e.g. the numbers displayed
- besides each slider. Here, 3 updates per second, or 300 ms is
- enough. This value is purely a user interface update rate and
- does not affect measurements in any way. (e.g. 300E-3).
- measurements_period:
- type: np.float64
- unit: s
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: s
- description: |
- The Measurements period is the integration time for precise
- measurements (averaging over specified period), mostly used
- in sweep modules. Examples are recording of a force-distance
- curve or a resonance of a cantilever. For fast measurements
- with small steps, a value of 40 ms may be reasonable. For
- normal use, 300-500 ms is a good value, but for recording a
- resonance of a high-Q cantilever, values of several seconds
- might be necessary. Usually this parameter doesn \u2019t need
- to be set from this module; the sweep modules will set this
- value according to the sweep timings. (e.g. 500E-3) "
- Scan_control:
- section:
- m_annotations:
- eln:
- overview: true
- sub_sections:
- Roi:
- section:
- m_annotations:
- eln:
- overview: true
- # TODO: Confirm it.
- quantities:
- frame:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- description: |
- Also clarify the frame for the ROI of the scan (should depend
- on the lab frame).
- Circuit:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- channels_current:
- type: str
- unit: A
- m_annotations:
- eln:
- component: StringEditQuantity
- defaultDisplayUnit: A
- description: |
- The scan channels are selected by users. (e.g. (A);Bias (V);Z
- (m);LI Demod 2 X (A); LI 2 Y (A);LI Demod 1 X (A);
- LI Demod 1 Y (A)).
- Positioner:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- scanfield:
- type: np.float64
- m_annotations:
- eln:
- component: NumberEditQuantity
- description: |
- Configure the scan frame like x position; y position; width;
- height. (e.g. 3.11737E-9;29.1583E-9;15E-9;15E-9;0E+0) '
- pixels_line:
- type: np.float64
- m_annotations:
- eln:
- component: NumberEditQuantity
- description: |
- Scan resolution by setting the Lines equal to Pixels. (e.g. 512) '
- lines:
- type: np.float64
- m_annotations:
- eln:
- component: NumberEditQuantity
- description: |
- Define the image resolution. (e.g. 512).
- speed_forw:
- type: np.float64
- unit: m/s
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: m/s
- description: |
- Define the scan forward speed in the forward direction. (m/s)
- (e.g. 11.7187E-9).
- speed_backw:
- type: np.float64
- unit: m/s
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: m/s
- description: |
- Define the scan backward speed in the forward direction. (m/s)
- (e.g. 11.7187E-9) '
- quantities:
- stm_head_temp:
- type: np.float64
- unit: K
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: K
- description: |
- Temperature of STM head. Note: At least one field from stm_head_temperature,
- cryo_bottom_temp and cryo_sheild_temp must be provided. '
- cryo_bottom_temp:
- type: np.float64
- unit: K
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: K
- description: |
- Temperature of LHe helium cryostat. Note: At least one field from
- stm_head_temperature, cryo_bottom_temp and cryo_sheild_temp must be provided.
- cryo_shield_temp:
- type: np.float64
- unit: K
- m_annotations:
- eln:
- component: NumberEditQuantity
- defaultDisplayUnit: K
- description: |
- Temperature of LN2 nitrogen shield. Temperature 3 (K) (e.g 78.00000E+0). Note:
- At least one field from stm_head_temperature, cryo_bottom_temp and
- cryo_sheild_temp must be provided.
- sample:
- section:
- m_annotations:
- eln:
- overview: true
- quantities:
- name:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- description: |
- Name of the sample.
- sample_prep_descripton:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- description: |
- At this moment no base class available that can track entire sample preparation.
diff --git a/examples/data/stm/STS.scheme.archive.yaml b/examples/data/sts/common_files/STS.scheme.archive.yaml
similarity index 79%
rename from examples/data/stm/STS.scheme.archive.yaml
rename to examples/data/sts/common_files/STS.scheme.archive.yaml
index 0850c788874e27aa0be9548e0e54eb0c6dc74cd2..23e0980b83835e56fdf62c5633db132f99b1ca43 100644
--- a/examples/data/stm/STS.scheme.archive.yaml
+++ b/examples/data/sts/common_files/STS.scheme.archive.yaml
@@ -1,5 +1,5 @@
definitions:
- name: Eln example for NXiv_sweep2
+ name: Eln example for STM/STS (Scanning Tunneling Microscopy / Scanning Tunneling Spectroscopy)
sections:
stm:
base_sections:
@@ -12,8 +12,15 @@ definitions:
eln:
hide: []
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot (e.g. backward, forward) to be displayed on the entry of NeXus file
definition:
- type:
+ type:
type_kind: Enum
type_data:
- NXsts
@@ -93,28 +100,73 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
name:
type: str
m_annotations:
eln:
component: StringEditQuantity
description: |
- Name of the hardware. (e.g. Nanonis BP5e).
+ Name of the hardware. (e.g. Nanonis).
+ model:
+ type:
+ type_kind: Enum
+ type_data:
+ - Generic 5e
+ m_annotations:
+ eln:
+ component: EnumEditQuantity
+ description: |
+ Version or model of the component named by the manufacturer (e.g. Nanonis).
+ # TODO add option for model
+ model/@version:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ If model has a distinquishable version (e.g. BP5e).
+ # TODO add option for model/@version
software:
section:
m_annotations:
eln:
overview: true
quantities:
- version:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
+ model:
+ type:
+ type_kind: Enum
+ type_data:
+ - Generic
+ m_annotations:
+ eln:
+ component: EnumEditQuantity
+ description: |
+ Version or model of the component named by the manufacturer.
+ model/@version:
type:
type_kind: Enum
type_data:
- Generic 5e
+ - Generic 4.5
m_annotations:
eln:
component: EnumEditQuantity
- description: Version of the software.
+ description: |
+ If model has a distinquishable version.
vendor:
type:
type_kind: Enum
@@ -142,6 +194,13 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
amplification_factor:
type: np.float64
m_annotations:
@@ -155,6 +214,13 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
status:
type:
type_kind: Enum
@@ -183,11 +249,11 @@ definitions:
component: NumberEditQuantity
defaultDisplayUnit: Hz
description: |
- The signal is modulated by adding the frequency of the sine modulation. The
- modulation frequency spans can be from 10 mHz to 40 kHz, corresponding to the output filter
- cut-off range. When dealing with harmonics, it's essential to ensure that the
- harmonic frequencies remain below ~100 kHz, which aligns with the input filter cut-off.
- Be mindful that hardware filters might impact the amplitude as the signal approaches
+ The signal is modulated by adding the frequency of the sine modulation. The
+ modulation frequency spans can be from 10 mHz to 40 kHz, corresponding to the output filter
+ cut-off range. When dealing with harmonics, it's essential to ensure that the
+ harmonic frequencies remain below ~100 kHz, which aligns with the input filter cut-off.
+ Be mindful that hardware filters might impact the amplitude as the signal approaches
their cut-off frequencies (e.g. 973E+0).
modulation_amplitude:
type: np.float64
@@ -200,7 +266,7 @@ definitions:
The amplitude (in physical units of modulated signal) of the sine modulation.
demodulated_signal:
type: np.float64
- unit: A
+ unit: A
m_annotations:
eln:
component: NumberEditQuantity
@@ -222,6 +288,13 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
bias:
type: np.float64
unit: V
@@ -236,11 +309,11 @@ definitions:
eln:
component: NumberEditQuantity
bias_offset:
- type: str
+ type: np.float64
unit: V
m_annotations:
eln:
- component: StringEditQuantity
+ component: NumberEditQuantity
defaultDisplayUnit: V
description: ''
piezo_config:
@@ -249,6 +322,13 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
active_calib:
type: str
m_annotations:
@@ -261,7 +341,6 @@ definitions:
m_annotations:
eln:
component: BoolEditQuantity
- defaultDisplayUnit: on/off
description: |
Use the button to turn on/off the drift compensation. (e.g. FALSE).
Environment:
@@ -269,6 +348,14 @@ definitions:
m_annotations:
eln:
overview: true
+ quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
sub_sections:
Current_sensor:
section:
@@ -276,6 +363,13 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
current:
type: np.float64
unit: A
@@ -311,6 +405,13 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
x:
type: np.float64
unit: m
@@ -345,6 +446,13 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
z:
type: np.float64
unit: m
@@ -368,6 +476,13 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
integration_time:
type: np.float64
unit: s
@@ -433,6 +548,13 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
rt_frequency:
type: np.float64
unit: Hz
@@ -520,14 +642,29 @@ definitions:
m_annotations:
eln:
overview: true
+ quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
sub_sections:
Roi:
section:
m_annotations:
eln:
overview: true
- # TODO: Confirm it.
+ # TODO: Confirm it.
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
frame:
type: str
m_annotations:
@@ -542,6 +679,13 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
channels_current:
type: str
unit: A
@@ -559,6 +703,13 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
scanfield:
type: np.float64
m_annotations:
@@ -602,6 +753,13 @@ definitions:
Define the scan backward speed in the forward direction. (m/s)
(e.g. 11.7187E-9) '
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
stm_head_temp:
type: np.float64
unit: K
@@ -639,6 +797,13 @@ definitions:
eln:
overview: true
quantities:
+ default:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ description: |
+ The name of the default plot or group.
name:
type: str
m_annotations:
diff --git a/examples/data/sts/output.nxs b/examples/data/sts/output.nxs
deleted file mode 100644
index d4fd18a4a8e788516b69616d2458177ffecc9bb3..0000000000000000000000000000000000000000
Binary files a/examples/data/sts/output.nxs and /dev/null differ
diff --git a/examples/data/stm/STM_nanonis_generic_5e.sxm b/examples/data/sts/stm/STM_nanonis_generic_5e.sxm
similarity index 100%
rename from examples/data/stm/STM_nanonis_generic_5e.sxm
rename to examples/data/sts/stm/STM_nanonis_generic_5e.sxm
diff --git a/examples/data/stm/config_file_for_sxm.json b/examples/data/sts/stm/config_file_for_sxm.json
similarity index 98%
rename from examples/data/stm/config_file_for_sxm.json
rename to examples/data/sts/stm/config_file_for_sxm.json
index 73dd17397f9339f531ee514148191d002dd338cf..7a69f1fe0a12f8cf99765dd3e57094883ece9641 100644
--- a/examples/data/stm/config_file_for_sxm.json
+++ b/examples/data/sts/stm/config_file_for_sxm.json
@@ -61,7 +61,7 @@
"/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/sweep_control/circuit/indicators_period": "/NanonisMain/Indicators Period",
"/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/sweep_control/circuit/indicators_period/@units": "/NanonisMain/Indicators Period/@unit",
"/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/sweep_control/circuit/measurements_period": "/NanonisMain/Measurements Period",
- "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/sweep_control/circuit/measurements_period /@units": "/NanonisMain/Measurements Period/@unit",
+ "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/sweep_control/circuit/measurements_period/@units": "/NanonisMain/Measurements Period/@unit",
"/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/sweep_control/circuit/rt_frequency": "/NanonisMain/RT Frequency",
"/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/sweep_control/circuit/rt_frequency/@units": "/NanonisMain/RT Frequency/@unit",
"/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/sweep_control/circuit/signals_oversampling": "/NanonisMain/Signals Oversampling",
@@ -129,7 +129,6 @@
"unit":"/Piezo Configuration/Drift Z/@unit"}},
"/ENTRY[entry]/INSTRUMENT[instrument]/piezo_config/drift_correction_status": ["/Piezo Configuration/Drift correction status",
"/Piezo Calibration/Drift correction status"],
- "/ENTRY[entry]/INSTRUMENT[instrument]/piezo_config/drift_correction_status/@units": "/Piezo Configuration/Drift correction status/@unit",
"/ENTRY[entry]/INSTRUMENT[instrument]/piezo_config/hv_gain_N": {"X":{"value": "/Piezo Configuration/HV Gain X"},
"Y":{"value": "/Piezo Configuration/HV Gain Y"},
"Z":{"value": "/Piezo Configuration/HV Gain Z"}},
diff --git a/examples/data/stm/eln_data.yaml b/examples/data/sts/stm/eln_data.yaml
similarity index 52%
rename from examples/data/stm/eln_data.yaml
rename to examples/data/sts/stm/eln_data.yaml
index eb20b3718474f306babea847a75eccb7669548f1..4755c13f7127e8e73f4dffd53e5843b284dde679 100644
--- a/examples/data/stm/eln_data.yaml
+++ b/examples/data/sts/stm/eln_data.yaml
@@ -1,5 +1,17 @@
Instrument:
+ Environment:
+ Current_sensor: {}
+ Position:
+ z_controller: {}
+ Scan_control:
+ Circuit: {}
+ Positioner: {}
+ Roi: {}
+ Sweep_control: {}
+ current_amplifier: {}
hardware:
+ model: Generic 5e
+ model/@version: 5e
name: Nanonis
lock_in:
lock_in_data_flip_number: -1.0
@@ -19,20 +31,26 @@ Instrument:
bias_calibration: 1.0
bias_offset:
unit: V
- value: '0'
+ value: 0.0
software:
+ model: Generic
+ model/@version: Generic 5e
rt_release: '10771'
ui_release: '10771'
vendor: nanonis
- version: Generic 5e
stm_head_temp:
unit: K
value: 5.04866
collection_identifier: TiSe2_2303a_annealing_300C_5min_evaporate_Pyrene_1_
+default: backward
definition: NXsts
entry_identifier: TiSe2_2303a_annealing_300C_5min_evaporate_Pyrene_1_0070
-experiment_description: A new TiSe2, annealed at 300 C for 5 min, then cool down to
- RT, evaporate the Pyrene on RT, 2.2 E -7, totally 10 s.
-experiment_identifier: C:\Users\SPM-PEEM\Desktop\DATA_Nanonis\20220711_CreaTec_Service_Benchmarks_LHe\Nanonis-Session-PMD100-HVHU_CreaTec_Service_PalmaLabBerlin220711
+experiment_description: A new TiSe2, annealed at 300 C for 5 min, then cool down to RT,
+ evaporate the Pyrene on RT, 2.2 E -7, totally 10 s.
+experiment_identifier: 'C:\Users\SPM-PEEM\Desktop\DATA_Nanonis\20220711_CreaTec_Service_Benchmarks_LHe\Nanonis-Session-PMD100-HVHU_CreaTec_Service_PalmaLabBerlin220711
+ experiment_type: stm'
experiment_type: stm
+sample:
+ name: Test sample
+ sample_prep_descripton: This is a test sample to run a test experiment.
type: background
diff --git a/examples/data/sts/stm/stm_eln_example.archive.json b/examples/data/sts/stm/stm_eln_example.archive.json
new file mode 100644
index 0000000000000000000000000000000000000000..5adb0987c3f2e71dd051132fa9d2628035e39851
--- /dev/null
+++ b/examples/data/sts/stm/stm_eln_example.archive.json
@@ -0,0 +1 @@
+{"data":{"m_def":"../upload/raw/STS.scheme.archive.yaml#/definitions/section_definitions/0","nxdl":"NXsts","input_files":["STM_nanonis_generic_5e.sxm","config_file_for_sxm.json","eln_data.yaml"],"default":"backward","definition":"NXsts","experiment_type":"stm","type":"background","entry_identifier":"TiSe2_2303a_annealing_300C_5min_evaporate_Pyrene_1_0070","collection_identifier":"TiSe2_2303a_annealing_300C_5min_evaporate_Pyrene_1_","experiment_identifier":"C:\\Users\\SPM-PEEM\\Desktop\\DATA_Nanonis\\20220711_CreaTec_Service_Benchmarks_LHe\\Nanonis-Session-PMD100-HVHU_CreaTec_Service_PalmaLabBerlin220711 experiment_type: stm","experiment_description":"A new TiSe2, annealed at 300 C for 5 min, then cool down to RT, evaporate the Pyrene on RT, 2.2 E -7, totally 10 s.","Instrument":{"stm_head_temp":5.04866,"hardware":{"name":"Nanonis","model":"Generic 5e","model/@version":"5e"},"software":{"model":"Generic","model/@version":"Generic 5e","vendor":"nanonis","rt_release":"10771","ui_release":"10771"},"current_amplifier":{},"lock_in":{"status":"OFF","modulation_frequency":973,"modulation_amplitude":0.005,"lock_in_data_flip_number":-1},"sample_bias":{"bias":0.005,"bias_calibration":1,"bias_offset":0},"piezo_config":{"active_calib":"LHe"},"Environment":{"Current_sensor":{},"Position":{"z_controller":{}},"Sweep_control":{},"Scan_control":{"Roi":{},"Circuit":{},"Positioner":{}}}},"sample":{"name":"Test sample","sample_prep_descripton":"This is a test sample to run a test experiment."},"reader":"sts"}}
\ No newline at end of file
diff --git a/examples/data/sts/sts.zip b/examples/data/sts/sts.zip
deleted file mode 100644
index a4dab02d26ad49e89fd10982f805a04e50010fb7..0000000000000000000000000000000000000000
Binary files a/examples/data/sts/sts.zip and /dev/null differ
diff --git a/examples/data/sts/STS_nanonis_generic_5e_1.dat b/examples/data/sts/sts/STS_nanonis_generic_5e_1.dat
similarity index 100%
rename from examples/data/sts/STS_nanonis_generic_5e_1.dat
rename to examples/data/sts/sts/STS_nanonis_generic_5e_1.dat
diff --git a/examples/data/sts/config_file_for_dat.json b/examples/data/sts/sts/config_file_for_dat.json
similarity index 100%
rename from examples/data/sts/config_file_for_dat.json
rename to examples/data/sts/sts/config_file_for_dat.json
diff --git a/examples/data/sts/eln_data.yaml b/examples/data/sts/sts/eln_data.yaml
similarity index 55%
rename from examples/data/sts/eln_data.yaml
rename to examples/data/sts/sts/eln_data.yaml
index bfc1ab194582768eb6c82bb7dc550f8b86a33ace..75c57f434b06d13be5aade7ba0f96952dada28c5 100644
--- a/examples/data/sts/eln_data.yaml
+++ b/examples/data/sts/sts/eln_data.yaml
@@ -1,5 +1,19 @@
Instrument:
+ Environment:
+ Current_sensor: {}
+ Position:
+ z_controller: {}
+ Scan_control:
+ Circuit: {}
+ Positioner: {}
+ Roi: {}
+ Sweep_control:
+ Bias_spectroscopy: {}
+ circuit: {}
+ current_amplifier: {}
hardware:
+ model: Generic 5e
+ model/@version: BP5e
name: Nanonis BP5e
lock_in:
lock_in_data_flip_number: -1.0
@@ -11,7 +25,7 @@ Instrument:
value: 973.0
modulation_signal:
unit: V
- value: 973.0
+ value: 0.05
status: 'ON'
piezo_config:
active_calib: LHe
@@ -22,21 +36,26 @@ Instrument:
bias_calibration: 1.0
bias_offset:
unit: V
- value: '0'
+ value: 0.0
software:
+ model: Generic
+ model/@version: Generic 5e
rt_release: '10771'
ui_release: '10771'
vendor: nanonis
- version: Generic 5e
stm_head_temp:
unit: K
value: 4.92997
collection_identifier: 221122_Au_5K
+default: li_demod_1_x
definition: NXsts
entry_identifier: 221122_Au_5K00014
-experiment_description: 'Bias Spectroscopy: SYNC & Filter LP 8order WITHDRAW 600
- steps, locked Au(111), 50pA, 100 mV set point, 1mV DCA, 973Hz,138 1st
- H, -84 2nd H'
+experiment_description: '''Bias Spectroscopy: SYNC & Filter LP 8order WITHDRAW 600 steps,
+ locked Au(111), 50pA, 100 mV set point, 1mV DCA, 973Hz,138 1st H,
+ -84 2nd H'''
experiment_identifier: C:\Users\SPM-PEEM\Desktop\DATA_Nanonis\20220711_CreaTec_Service_Benchmarks_LHe\Nanonis-Session-PMD100-HVHU_CreaTec_Service_PalmaLabBerlin220711
experiment_type: sts
+sample:
+ name: Test Sample
+ sample_prep_descripton: This is a test sample for test experiment.
type: background
diff --git a/examples/data/sts/sts/sts_eln_example.archive.json b/examples/data/sts/sts/sts_eln_example.archive.json
new file mode 100644
index 0000000000000000000000000000000000000000..3ac1855ac772bd40477dd0583be8bf4f9f7d6411
--- /dev/null
+++ b/examples/data/sts/sts/sts_eln_example.archive.json
@@ -0,0 +1 @@
+{"data":{"m_def":"../upload/raw/STS.scheme.archive.yaml#/definitions/section_definitions/0","reader":"sts","nxdl":"NXsts","input_files":["STS_nanonis_generic_5e_1.dat","config_file_for_dat.json","eln_data.yaml"],"default":"li_demod_1_x","definition":"NXsts","experiment_type":"sts","type":"background","entry_identifier":"221122_Au_5K00014","collection_identifier":"221122_Au_5K","experiment_identifier":"C:\\Users\\SPM-PEEM\\Desktop\\DATA_Nanonis\\20220711_CreaTec_Service_Benchmarks_LHe\\Nanonis-Session-PMD100-HVHU_CreaTec_Service_PalmaLabBerlin220711","experiment_description":"'Bias Spectroscopy: SYNC & Filter LP 8order WITHDRAW 600 steps, locked Au(111), 50pA, 100 mV set point, 1mV DCA, 973Hz,138 1st H, -84 2nd H'","Instrument":{"stm_head_temp":4.92997,"hardware":{"name":"Nanonis BP5e","model":"Generic 5e","model/@version":"BP5e"},"software":{"model":"Generic","model/@version":"Generic 5e","vendor":"nanonis","rt_release":"10771","ui_release":"10771"},"current_amplifier":{},"lock_in":{"status":"ON","modulation_signal":0.05,"modulation_frequency":973,"modulation_amplitude":0.002,"lock_in_data_flip_number":-1},"sample_bias":{"bias":0.1,"bias_calibration":1,"bias_offset":0},"piezo_config":{"active_calib":"LHe"},"Environment":{"Current_sensor":{},"Position":{"z_controller":{}},"Sweep_control":{"Bias_spectroscopy":{},"circuit":{}},"Scan_control":{"Roi":{},"Circuit":{},"Positioner":{}}}},"sample":{"name":"Test Sample","sample_prep_descripton":"This is a test sample for test experiment."}}}
\ No newline at end of file
diff --git a/examples/data/sts/sts_example.archive.json b/examples/data/sts/sts_example.archive.json
deleted file mode 100644
index cda3e478dd9b1794ae150ebcca67d556684b2f5d..0000000000000000000000000000000000000000
--- a/examples/data/sts/sts_example.archive.json
+++ /dev/null
@@ -1 +0,0 @@
-{"data":{"m_def":"../upload/raw/STS.scheme.archive.yaml#/definitions/section_definitions/0","reader":"sts","nxdl":"NXsts","input_files":["STS_nanonis_generic_5e_1.dat","config_file_for_dat.json","eln_data.yaml"],"definition":"NXsts","experiment_type":"sts","type":"background","entry_identifier":"221122_Au_5K00014","collection_identifier":"221122_Au_5K","experiment_identifier":"C:\\Users\\SPM-PEEM\\Desktop\\DATA_Nanonis\\20220711_CreaTec_Service_Benchmarks_LHe\\Nanonis-Session-PMD100-HVHU_CreaTec_Service_PalmaLabBerlin220711","experiment_description":"Bias Spectroscopy: SYNC & Filter LP 8order WITHDRAW 600 steps, locked Au(111), 50pA, 100 mV set point, 1mV DCA, 973Hz,138 1st H, -84 2nd H","Instrument":{"stm_head_temp":4.92997,"hardware":{"name":"Nanonis BP5e"},"software":{"version":"Generic 5e","vendor":"nanonis","rt_release":"10771","ui_release":"10771"},"lock_in":{"status":"ON","lock_in_data_flip_number":-1,"modulation_signal":973,"modulation_frequency":973,"modulation_amplitude":0.002},"sample_bias":{"bias":0.1,"bias_calibration":1,"bias_offset":"0"},"piezo_config":{"active_calib":"LHe"}}}}
diff --git a/scripts/generate_example_uploads.sh b/scripts/generate_example_uploads.sh
index 64a8c412650e97264de739d496415e64c89a63ea..40fd6c317bf4550cc0918fa39b8e7c24a5c85aee 100755
--- a/scripts/generate_example_uploads.sh
+++ b/scripts/generate_example_uploads.sh
@@ -25,5 +25,5 @@ zip -r -j uploads/em_om.zip em_om/*
zip -r -j uploads/em_nion.zip em_nion/*
zip -r -j uploads/iv_temp.zip iv_temp/*
zip -r -j uploads/xps.zip xps/*
-zip -r -j uploads/sts.zip sts/*
-zip -r -j uploads/stm.zip stm/*
+zip -r -j uploads/sts.zip sts/sts/* sts/common_files/*
+zip -r -j uploads/stm.zip sts/stm/* sts/common_files/*