Instamatic can be configured through a series of yaml files. global.yaml at the root of the config directory, and three subdirectories (microscope, calibration, camera) that hold the specific configuration for the microscope set up.
By default, instamatic looks for the config directory in %APPDATA%/Instamatic. This directory is created automatically with the default config files on first use. The config directory is printed when the program is started. The default location can be overriden using the Instamatic environment variable, i.e. in Powershell: $ENV:Instamatic = "C:/Instamatic". In the portable installation, the config directory is in the root directory as defined by the Instamatic environment variable.
You can run:
instamatic.autoconfig.exeTo help generate some of the input files (in particular templates for the microscope/calibration files).
Examples of configuration files can be found here.
This is the global configuration file for instamatic. It defines which microscope / camera setup to use through the microscope, camera, and calibration settings.
microscope
name of the microscope calibration file use. For example, if this is set to jeol-2100, instamatic will look for the config file jeol-2100.yaml in the config/microscope directory.
camera
name of the camera file to use. Instamatic will look for the corresponding .yaml in the config/camera directory.
calibration
name of the calibration file to use. Instamatic will look for the corresponding .yaml file in the config/calibration directory.
data_directory
Default path to where data should be stored, i.e. C:/instamatic
flatfield
Path to tiff file containing flatfield, i.e. C:/instamatic/flatfield.tiff. Leave blank if no flatfield should be applied.
use_tem_server
use the tem server with the given host/port below. If instamatic cannot find the tem server, it will start a new temserver in a subprocess. The tem server can be started using instamatic.temserver.exe. This helps to isolate the microscope communication. Instamatic will connect to the server via sockets. The main advantage is that a socket client can be run in a thread, whereas a COM connection makes problems if it is not in main thread.
tem_server_host
Set this to localhost if the TEM server is run locally. To make a remote connection over the network, use '0.0.0.0' on the server, and the ip address of the server on the client.
tem_server_port
the server port, default: 8088
indexing_server_exe
After data are collected, the path where the data are saved can be sent to this program via a socket connection for automated data processing. Available are the dials indexing server (instamatic.dialsserver.exe) and the XDS indexing server (instamatic.xdsserver.exe)
indexing_server_host
IP to use for the indexing server, similar to above.
indexing_server_port
Port to use for the indexing server, default: 8089
dials_script
The script that is run when the dials indexing server is used.
cred_relax_beam_before_experiment
Relax the beam before a CRED experiment (for testing only), default: false
cred_track_stage_positions
Track the stage position during a CRED experiment (for testing only), default: false
modules
List of modules to load for the GUI, must be one of {cred, cred_tvips, cred_fei, sed, autocred, red, machine_learning, ctrl, debug, about, io}
In this file the calibration of the pixelsizes can be specified, both in diffraction and imaging modes. This file is must be located the config/calibration directory, and can have any name as defined in global.yaml. To begin with, the values can be safely set to 1.0, as their importance depends on the experiment you are running.
name
Name of the corresponding camera interface. This variable is not used currently in the code at present.
pixelsize_diff
Give here a list of camera lengths (as reported by the TEM) and the corresponding pixel dimensions in reciprocal angstrom, separated by a :, for example:
150: 0.02942304
200: 0.02206728
250: 0.017653824
...
pixelsize_lowmag
Give here the magnification and pixel size for images taken in lowmag mode in nanometer, for example:
50: 895.597
80: 559.748
100: 447.799
...
pixelsize_mag1
Likewise, give here the magnification and pixel size for the images taken in mag1 mode in nanometer, for exmaple:
2500: 16.2926
3000: 13.3909
4000: 9.87389
...
Optionally, tables for pixelsize_mag2, pixelsize_samag can also be defined, but they are not used.
This file holds the specifications of the camera. This file is must be located the config/camera directory, and can have any name as defined in global.yaml.
name
Give the name of the camera interface to connect to, for example: timepix/emmenu/simulate/gatan. Leave blank to load the camera specs, but do not load the camera module (this also turns off the videostream gui).
default_binsize
Set the default binsize, default: 1
default_exposure
Set the default exposure in seconds, i.e. 0.02
dimensions
Give the dimensions of the camera at binning 1, for example: [516, 516]
dynamic_range
Give the maximum counts of the camera, for example: 11800
physical_pixelsize
The physical size of a pixel in micrometer, for example: 0.055
possible_binsizes
Give here a list of possible binnings, for example: [1] or [1, 2, 4]
camera_rotation_vs_stage_xy
In radians, give here the rotation of the position of the rotation axis with respect to the
horizontal. Corresponds to the rotation axis in RED and PETS, for example: -2.24. You can find the rotation axis for your setup using the script edtools.find_rotation_axis available from here.
stretch_amplitude
Use instamatic.stretch_correction to characterize the lens distortion. The numbers here are used to calculate the XCORR/YCORR maps. The amplitude is the percentage difference between the maximum and minimum eigenvectors of the ellipsoid, i.e. if the amplitude is 2.43, eig(max)/eig(min) = 1.0243. You can use the program instamatic.stretch_correction available here on some powder patterns to define these numbers.
stretch_azimuth
The azimuth is gives the direction of the maximum eigenvector with respect to the horizontal X-axis (pointing right) in degrees, for example: 83.37
correction_ratio
Set the correction ratio for the cross pixels in the Timepix detector, default: 3
calib_beamshift
Set up the grid and stepsize for the calibration of the beam shift in SerialED. The calibration will run a grid of stepsize by stepsize points, with steps of stepsize. The stepsize must be given corresponding to 2500x, and instamatic will then adjust the stepsize depending on the actual magnification, if needed. For example:
{gridsize: 5, stepsize: 500}
calib_directbeam
Set up the grid and stepsize for the calibration of the direct beam in diffraction mode, for example:
BeamShift: {gridsize: 5, stepsize: 300}
DiffShift: {gridsize: 5, stepsize: 300}
This file holds all the specifications of the microscope as necessary. It is important to set up the camera lengths, magnifications, and magnification modes. This file is must be located the microscope/camera directory, and can have any name as defined in global.yaml.
name
name of the microscope interface to use
wavelength
The wavelength of the microscope in Ansgtroms. This is used to generate some of the output files after data collection, i.e. for 120kV: 0.033492, 200kV: 0.025079, or 300 kV: 0.019687. A useful website to calculate the de Broglie wavelength is here.
range_diff
List here the available camera lengts available on the microscope in ascending order
range_diff: [150, 200, 250, 300, 400, 500, 600, 800, 1000, 1200,
1500, 2000, 2500, 3000, 3500, 4000, 4500]
range_mag1, range_lowmag, range_mag2, range_samag
List here the available magnifications available on the microscope in ascending order, for example:
range_mag1: [2000, 2500, 3000, 4000, 5000, 6000, 8000, 10000, 12000,
15000, 20000, 25000, 30000, 40000, 50000, 60000, 80000, 100000, 120000, 150000,
200000, 250000, 300000, 400000, 500000, 600000, 800000, 1000000, 1200000, 1500000,
2000000]