Block diagram
A native file format of NT-MDT scientific software. Usually contains any of:
Some examples of mdt files can be downloaded at:
This page hosts a formal specification of NT-MDT data using Kaitai Struct. This specification can be automatically translated into a variety of programming languages to get a parsing library.
meta:
id: nt_mdt
title: NT-MDT data
application:
- Nova
- Image Analysis
- NanoEducator
- Gwyddion
- Callisto
file-extension: mdt
license: GPL-3.0-or-later
endian: le
doc: |
A native file format of NT-MDT scientific software. Usually contains
any of:
* [Scanning probe](https://en.wikipedia.org/wiki/Scanning_probe_microscopy) microscopy scans and spectra
* [Raman spectra](https://en.wikipedia.org/wiki/Raman_spectroscopy)
* results of their analysis
Some examples of mdt files can be downloaded at:
* <https://www.ntmdt-si.ru/resources/scan-gallery>
* <http://callistosoft.narod.ru/Resources/Mdt.zip>
doc-ref: https://svn.code.sf.net/p/gwyddion/code/trunk/gwyddion/modules/file/nt-mdt.c
seq:
- id: signature
contents: [0x01, 0xb0, 0x93, 0xff]
- id: size
type: u4
doc: File size (w/o header)
- id: reserved0
size: 4
- id: last_frame
type: u2
- id: reserved1
size: 18
- id: wrond_doc
size: 1
doc: "documentation specifies 32 bytes long header, but zeroth frame starts at 33th byte in reality"
- id: frames
size: size
type: framez
types:
uuid:
seq:
- id: data
type: u1
repeat: expr
repeat-expr: 16
framez:
seq:
- id: frames
type: frame
repeat: expr
repeat-expr: '_root.last_frame+1'
title:
seq:
- id: title_len
type: u4
- id: title
type: str
encoding: cp1251
size: title_len
xml:
seq:
- id: xml_len
type: u4
- id: xml
type: str
encoding: UTF-16LE
size: xml_len
version:
seq:
- id: minor
type: u1
- id: major
type: u1
frame:
seq:
- id: size
type: u4
doc: "h_sz"
- id: main
type: frame_main
size: size - 4
enums:
frame_type:
0: scanned
1: spectroscopy
3: text
105: old_mda
106: mda
107: palette
190: curves_new
201: curves
types:
date_time:
seq:
- id: date
type: date
- id: time
type: time
types:
date:
seq:
- id: year
type: u2
doc: "h_yea"
- id: month
type: u2
doc: "h_mon"
- id: day
type: u2
doc: "h_day"
time:
seq:
- id: hour
type: u2
doc: "h_h"
- id: min
type: u2
doc: "h_m"
- id: sec
type: u2
doc: "h_s"
frame_main:
seq:
- id: type
type: u2
enum: frame_type
doc: "h_what"
- id: version
type: version
- id: date_time
type: date_time
- id: var_size
type: u2
doc: "h_am, v6 and older only"
- id: frame_data
-orig-id: dataframe
size-eos: true
type:
switch-on: type
cases:
'frame_type::scanned': fd_scanned
'frame_type::mda': fd_meta_data
'frame_type::spectroscopy': fd_spectroscopy
'frame_type::curves': fd_spectroscopy
'frame_type::curves_new': fd_curves_new
doc: ""
dots:
seq:
- id: fm_ndots
type: u2
- id: coord_header
-orig-id: coordheader
type: dots_header
if: fm_ndots > 0
- id: coordinates
type: dots_data
repeat: expr
repeat-expr: fm_ndots
- id: data
type: data_linez(_index)
repeat: expr
repeat-expr: fm_ndots
types:
dots_header:
seq:
- id: header_size
-orig-id: headersize
type: s4
- id: header
size: header_size
type: header_
types:
header_:
seq:
- id: coord_size
-orig-id: coordsize
type: s4
- id: version
type: s4
- id: xyunits
type: s2
enum: unit
dots_data:
seq:
- id: coord_x
type: f4
- id: coord_y
type: f4
- id: forward_size
type: s4
- id: backward_size
type: s4
data_linez:
params:
- id: index
type: u2
seq:
- id: forward
type: s2
repeat: expr
repeat-expr: _parent.coordinates[index].forward_size
- id: backward
type: s2
repeat: expr
repeat-expr: _parent.coordinates[index].backward_size
axis_scale:
seq:
- id: offset
type: f4
doc: "x_scale->offset = gwy_get_gfloat_le(&p);# r0 (physical units)"
- id: step
type: f4
doc: >
x_scale->step = gwy_get_gfloat_le(&p);
r (physical units)
x_scale->step = fabs(x_scale->step);
if (!x_scale->step) {
g_warning("x_scale.step == 0, changing to 1");
x_scale->step = 1.0;
}
- id: unit
type: s2 # x_scale->unit = (gint16)gwy_get_guint16_le(&p);
enum: unit
doc: "U"
fd_curves_new:
seq:
- id: block_count
type: u4
- id: blocks_headers
type: block_descr
repeat: expr
repeat-expr: block_count
- id: blocks_names
type: str
encoding: UTF-8
size: blocks_headers[_index].name_len
repeat: expr
repeat-expr: block_count
- id: blocks_data
size: blocks_headers[_index].len
repeat: expr
repeat-expr: block_count
types:
block_descr:
seq:
- id: name_len
type: u4
- id: len
type: u4
fd_spectroscopy:
seq:
- id: vars
type: vars
size: _parent.var_size
- id: fm_mode
type: u2
- id: fm_xres
type: u2
- id: fm_yres
type: u2
- id: dots
type: dots
- id: data
type: s2
repeat: expr
repeat-expr: fm_xres*fm_yres
- id: title
type: title
- id: xml
type: xml
types:
vars:
seq:
- id: x_scale
type: axis_scale
- id: y_scale
type: axis_scale
- id: z_scale
type: axis_scale
- id: sp_mode
type: u2
- id: sp_filter
type: u2
- id: u_begin
type: f4
- id: u_end
type: f4
- id: z_up
type: s2
- id: z_down
type: s2
- id: sp_averaging
type: u2
- id: sp_repeat
type: u1 # bool
- id: sp_back
type: u1 # bool
- id: sp_4nx
type: s2
- id: sp_osc
type: u1 # bool
- id: sp_n4
type: u1
- id: sp_4x0
type: f4
- id: sp_4xr
type: f4
- id: sp_4u
type: s2
- id: sp_4i
type: s2
- id: sp_nx
type: s2
fd_meta_data:
seq:
- id: head_size
type: u4
- id: tot_len
type: u4
- id: guids
type: uuid
repeat: expr
repeat-expr: 2
- id: frame_status
size: 4
- id: name_size
type: u4
- id: comm_size
type: u4
- id: view_info_size
type: u4
- id: spec_size
type: u4
- id: source_info_size
type: u4
- id: var_size
type: u4
- id: data_offset
type: u4
- id: data_size
type: u4
- id: title
type: str
size: name_size
encoding: UTF-8
- id: xml
type: str
size: comm_size
encoding: UTF-8
- id: struct_len
type: u4
- id: array_size
type: u8
- id: cell_size
type: u4
- id: n_dimensions
type: u4
- id: n_mesurands
type: u4
- id: dimensions
type: calibration
repeat: expr
repeat-expr: n_dimensions
- id: mesurands
type: calibration
repeat: expr
repeat-expr: n_mesurands
instances:
image:
pos: data_offset
type: image
size: data_size
types:
image:
seq:
- id: image
type: vec
repeat: eos
types:
vec:
seq:
- id: items
type:
switch-on: _parent._parent.mesurands[_index].data_type
cases:
"data_type::uint8": u1
"data_type::uint16": u2
"data_type::uint32": u4
"data_type::uint64": u8
"data_type::int8": s1
"data_type::int16": s2
"data_type::int32": s4
"data_type::int64": s8
"data_type::float32": f4
"data_type::float64": f8
#"data_type::float48": s8
#"data_type::float80": s8
#"data_type::floatfix": s8
repeat: expr
repeat-expr: _parent._parent.n_mesurands
calibration:
seq:
- id: len_tot
type: u4
- id: len_struct
type: u4
- id: len_name
type: u4
- id: len_comment
type: u4
- id: len_unit
type: u4
- id: si_unit
type: u8
- id: accuracy
type: f8
- id: function_id_and_dimensions
type: u8
- id: bias
type: f8
- id: scale
type: f8
- id: min_index
type: u8
- id: max_index
type: u8
- id: data_type
type: s4
enum: data_type
- id: len_author
type: u4
- id: name
type: str
encoding: utf-8
size: len_name
- id: comment
type: str
encoding: utf-8
size: len_comment
- id: unit
type: str
encoding: utf-8
size: len_unit
- id: author
type: str
encoding: utf-8
size: len_author
instances:
count:
-orig-id: nx, ny and nz
value: max_index - min_index + 1
fd_scanned:
seq:
- id: vars
type: vars
size: _parent.var_size
- id: orig_format
type: u4
doc: "s_oem"
if: false
- id: tune
type: u4
enum: lift_mode
doc: "z_tune"
if: false
- id: feedback_gain
type: f8
doc: "s_fbg"
if: false
- id: dac_scale
type: s4
doc: "s_s"
if: false
- id: overscan
type: s4
doc: "s_xov (in %)"
if: false
#Frame mode stuff
- id: fm_mode
type: u2
doc: "m_mode"
- id: fm_xres
type: u2
doc: "m_nx"
- id: fm_yres
type: u2
doc: "m_ny"
- id: dots
type: dots
- id: image
type: s2
repeat: expr
repeat-expr: fm_xres * fm_yres
#Stuff after data
- id: title
type: title
- id: xml
type: xml
types:
vars:
seq:
- id: x_scale
type: axis_scale
- id: y_scale
type: axis_scale
- id: z_scale
type: axis_scale
- id: channel_index
type: u1
enum: adc_mode
doc: "s_mode"
- id: mode
type: u1
enum: mode
doc: "s_dev"
- id: xres
type: u2
doc: "s_nx"
- id: yres
type: u2
doc: "s_ny"
- id: ndacq
type: u2
doc: "Step (DAC)"
- id: step_length
type: f4
doc: "s_rs in Angstrom's (Angstrom*gwy_get_gfloat_le(&p))"
- id: adt
type: u2
doc: "s_adt"
- id: adc_gain_amp_log10
type: u1
doc: "s_adc_a"
- id: adc_index
type: u1
doc: "ADC index"
#XXX: Some fields have different meaning in different versions
- id: input_signal_or_version
type: u1
doc: "MDTInputSignal smp_in; s_smp_in (for signal) s_8xx (for version)"
- id: substr_plane_order_or_pass_num
type: u1
doc: "s_spl or z_03"
- id: scan_dir
type: scan_dir
doc: "s_xy TODO: interpretation"
- id: power_of_2
type: u1
doc: "s_2n (bool)"
- id: velocity
type: f4 # frame->velocity = Angstrom*gwy_get_gfloat_le(&p);
doc: "s_vel (Angstrom/second)"
- id: setpoint
type: f4 # frame->setpoint = Nano*gwy_get_gfloat_le(&p);
doc: "s_i0"
- id: bias_voltage
type: f4 # frame->bias_voltage = gwy_get_gfloat_le(&p);
doc: "s_ut"
- id: draw
type: u1
doc: "s_draw (bool)"
- id: reserved
type: u1
- id: xoff
type: s4
doc: "s_x00 (in DAC quants)"
- id: yoff
type: s4
doc: "s_y00 (in DAC quants)"
- id: nl_corr
type: u1
doc: "s_cor (bool)"
dot:
seq:
- id: x
type: s2
- id: y
type: s2
scan_dir:
seq:
- id: unkn
type: b4
- id: double_pass
type: b1
- id: bottom
type: b1
doc: "Bottom - 1 Top - 0"
- id: left
type: b1
doc: "Left - 1 Right - 0"
- id: horizontal
type: b1
doc: "Horizontal - 1 Vertical - 0"
enums:
mode:
0: stm
1: afm
2: unknown2
3: unknown3
4: unknown4
input_signal:
0: extension_slot
1: bias_v
2: ground
lift_mode:
0: step
1: fine
2: slope
enums:
spm_technique:
0: contact_mode
1: semicontact_mode
2: tunnel_current
3: snom
data_type:
0: unknown0
'-1': int8
1: uint8
'-2': int16
2: uint16
'-4': int32
4: uint32
'-8': int64
8: uint64
'-5892': float32
'-9990': float48
'-13320': float64
'-16138': float80
'-65544': floatfix
xml_scan_location:
0: hlt
1: hlb
2: hrt
3: hrb
4: vlt
5: vlb
6: vrt
7: vrb
xml_param_type:
0: none
1: laser_wavelength
2: units
0xff: data_array
spm_mode:
0: constant_force
1: contact_constant_height
2: contact_error
3: lateral_force
4: force_modulation
5: spreading_resistance_imaging
6: semicontact_topography
7: semicontact_error
8: phase_contrast
9: ac_magnetic_force
10: dc_magnetic_force
11: electrostatic_force
12: capacitance_contrast
13: kelvin_probe
14: constant_current
15: barrier_height
16: constant_height
17: afam
18: contact_efm
19: shear_force_topography
20: sfom
21: contact_capacitance
22: snom_transmission
23: snom_reflection
24: snom_all
25: snom
adc_mode:
0xFF: off
0: height
1: dfl
2: lateral_f
3: bias_v
4: current
5: fb_out
6: mag
7: mag_sin #MAG*Sin
8: mag_cos #MAG*Cos
9: rms
10: calc_mag
11: phase1
12: phase2
13: calc_phase
14: ex1
15: ex2
16: hv_x
17: hv_y
18: snap_back
consts:
32: file_header_size
22: frame_header_size
8: frame_mode_size
30: axis_scales_size
77: scan_vars_min_size
38: spectro_vars_min_size
unit:
-10: raman_shift
-9: reserved0
-8: reserved1
-7: reserved2
-6: reserved3
-5: meter
-4: centi_meter
-3: milli_meter
-2: micro_meter
-1: nano_meter
0: angstrom
1: nano_ampere
2: volt
3: none
4: kilo_hertz
5: degrees
6: percent
7: celsius_degree # -orig-id: celsium_degree
8: volt_high
9: second
10: milli_second
11: micro_second
12: nano_second
13: counts
14: pixels
15: reserved_sfom0
16: reserved_sfom1
17: reserved_sfom2
18: reserved_sfom3
19: reserved_sfom4
20: ampere2
21: milli_ampere
22: micro_ampere
23: nano_ampere2
24: pico_ampere
25: volt2
26: milli_volt
27: micro_volt
28: nano_volt
29: pico_volt
30: newton
31: milli_newton
32: micro_newton
33: nano_newton
34: pico_newton
35: reserved_dos0
36: reserved_dos1
37: reserved_dos2
38: reserved_dos3
39: reserved_dos4