The structure sm_par

The sm_par structure contains information stored in data file headers, and also additional information that is derived from the data file header. It holds all the information which is necessary to understand the raw data from the data file.

The structure sm_par is used both in C++ and in IDL. The file defining the structure for C++ is sm_par.h, while the file used in IDL is sm_ipar_stxm5.pro; these files should be in rigid agreement with each other!

At the top of these files we define the following constants which are mainly used to define the number of elements for array parameters:

SM_PAR_ADC_PORTS = 16 The number of ADC channels

SM_PAR_SCALER_PORTS = 2 The number of scaler (counter) channels

SM_PAR_MAXPOINTLIST = 25 The maximum number of locations in the scan which can be labeled with a name

SM_PAR_STRLEN = 128 The standard (maximum) length of string parameters

In IDL, these constants can be specified as keywords. This is necessary if you want to read an old data file in which these constants might have been different.

What follows is a listing of all elements in the structure. In the C++ version, we precede each name with a type specifier.

strlen (I32): Maximum string length in characters (128).

n_adc_channels (I32): Number of ADC channels (16).

n_scaler_channels (I32): Number of scaler (counter) channels (2).

maxpointlist (I32): Maximum number of points in the pointlist. These are specific locations in the scan which can be labeled with a name (25).

filever (I32): Follows changes in the file format. When the file format is changed, the filever should be incremented.

fast_device, slow_device (I32): Code (integer number) for the fast and slow scan devices. The codes are set at the top of sm_par.h.

fast_device_name, slow_device_name (I8[SM_PAR_STRLEN]): String holding the name of the column and row devices, corresponding to the short name in the enumeration at the top of sm_par.h.

detector (I32): Code (integer number) for the detector used. The code is defined at the top of sm_par.h.

detector_name (I32[SM_PAR_STRLEN]): Name describing the detector used, corresponding to the short name in the enumeration at the top of sm_par.h.

fast_direction, slow_direction (I32): plus 1 if the corresponding axis was scanned into the positive direction, and minus 1 if is was scanned in the negative direction. Except ZOSA, and ZSTG only for the CRYO microscope, all scan directions are negative (for real image scans, this is required so that the scan image looks like the real sample in the VLM, or as looked at in the upstream direction).

n_fast_pixels, n_slow_pixels (I32): Number of pixels in the horizontal and vertical directions.

n_data (I32): Number of measurements (recorded detector channels) for each pixel.

pixel_channel_names (I8[(SM_PAR_N_ADC_CHANNELS+SM_PAR_N_SCALER_CHANNELS)* SM_PAR_STRLEN]): Array of strings describing the channels in the order as they are recorded in the data array. Only as many elements are filled as channels are recorded.

fast_pixel_um, slow_pixel_um (F64): Pixel size.

dwell_msec (F32): Desired dwell time (which was chosen by the user). In scans with a piezo as fast axis, this will correspond to the actual dwell time. When a stepper motor is used as fast axis, the actual dwell time will vary from pixel to pixel due to acceleration and deceleration of the stage. In that case, we record a clock signal for each pixel to determine the actual dwell time.

bidirectional (I32): Flag (0 or 1) telling whether the scan was taken bidirectional.

shutopen (I32): Flag (0 or 1) telling whether the shutter was open during the scan. In STXM 4, it was also used to tell when the shutter was closed for the first scan line, which was used for a quick and dirty silicon detector calibration.

tilt_degrees (F32): Tilt of sample for tomography.

x_center_um, y_center_um, z_center_um (F64): Center position of image (interferometer position).

x_pzt_um, y_pzt_um, x_stg_um, y_stg_um, z_stg_um, x_det_um, y_det_um, z_osa_um (F64): Position of all the stages.

start_ev, stop_ev (F64): Energy at start and end of scan.

adc_voltsperbit, adc_voltsoffset (F32[SM_PAR_N_ADC_CHANNELS]): ADC calibration.

counts_divideby (I32): Integer factor describing the divideby setting for the proportional counter. When reading data back in from a file, one must multiply by this number to obtain the true values (only for the proportional counter channel!).

clock_hertz (F32): In scans with a piezo as fast axis, the dwell time is rigidly fixed, so no clock will be recorded). Then, clock_hertz will hold the clock rate at which pixels are recorded, which is the inverse of the dwell time.

In scans where a stepping motor is the fast axis (due to acceleration and deceleration, the actual dwell time varies), we will record a clock signal as a separate detector channel, and clock_hertz will hold the clock rate (100 kHz or 20 MHz). dwell_msec in that case will hold the desired, but not the actual dwell time.

n_sidet_segments (I32): Number of segments on the silicon detector chip.

sidet_crosstalk_matrix (F32[SM_PAR_N_ADC_CHANNELS][SM_PAR_N_ADC_CHANNELS]): Crosstalk matrix for the segmented silicon detector

sidet_u0_mvolts (F32[SM_PAR_N_ADC_CHANNELS]): Voltage offset (extrapolated voltage for zero dwell time).

sidet_c_idark_mvolts_per_ms (F32[SM_PAR_N_ADC_CHANNELS]): C $\times$ I_dark factor.

sidet_mvolts_per_femtocoulomb (F32[SM_PAR_N_ADC_CHANNELS]): Sidet amplifier output per input charge.

sidet_photons_per_femtocoulomb (F32): Photon-charge conversion factor.

sidet_deadtime_ms (F32): Silicon detector dead time.

sidet_calibration_time (I8[SM_PAR_STRLEN]): String holding the time when the detector was last calibrated.

sidet_chip_name (I8[SM_PAR_STRLEN]): Name of the detector chip.

sidet_chipdesign (I8[SM_PAR_STRLEN]): String describing the silicon detector chip design.

disp_min, disp_max, disp_gamma (F32): Minimum, maximum and gamma values for the display at the time when the file was saved.

disp_name (I8[SM_PAR_STRLEN]): Name of the display which was shown when the file was saved. See the IDL routine displays.pro for a list of available displays.

microscope (I8[SM_PAR_STRLEN]): String describing the microscope (stxmi, stxmo, or cryo).

systime (I8[SM_PAR_STRLEN]): String of the time of the scan.

scientist, sample, comments1, comments2 (I8[SM_PAR_STRLEN]): Strings holding the name of the scientist(s), the sample and two arbitrary comments.

original_filename (I8[SM_PAR_STRLEN]): Name under which the file was originally saved. Don't change!

temp1_celsius, temp2_celsius (F32): Temperature readings 1 and 2 (mainly for cryo).

temp1_name, temp2_name (I8[SM_PAR_STRLEN]): Strings describing the temperature readings.

n_oneread_channels (I32): Number of channels which are read only once per scan.

oneread_data (I16[SM_PAR_N_ADC_CHANNELS]): Array of data which is read only once per scan (at end of scan).

oneread_channel_names (I8[SM_PAR_N_ADC_CHANNELS*SM_PAR_STRLEN]): Array of names for the oneread channels.

n_pointlist (I32): Number of valid entries in the pointlist (specific locations in the scan which can be labelled with a name).

point_namestr (I8[SM_PAR_MAXPOINTLIST*SM_PAR_STRLEN]): Array of strings holding the labels for the marked locations in the scan.

point_xpos, point_ypos (F32[SM_PAR_MAXPOINTLIST]): Arrays holding the X and Y positions of the marked locations in the scan.

ring_gev, ring_ma (F32): Storage ring parameters (read at end of scan).

undulator_gap_mm, undulator_period_mm (F32):

ens_slit_um, exs_slit_um, exsy_slit_um, exsh_slit_um, exsyh_slit_um (F64): Width of entrance and exit slits. h stands for the high energy exit slits on the inboard branch.

exs_slits_used (I32): Flag telling which set of exit slits were used (only meaningful for inboard branch). 0: normal, 1: high energy slits.

sgm_zero_order_steps, sgm_steps_per_angstrom (F32): Monochromator calibration parameters.

zp_d_um, zp_delta_nm, zp_stop_um, osa_d_um (F64): Zone plate and OSA parameters.

zp_name (I8[SM_PAR_STRLEN]): Name of the zone plate.