Hiding and Disabling Menu and Dialog Items

This page describes the mechanism for hiding or disabling menu items and dialog elements in SerialEM.  This can be done either to prevent users from doing some operations, or to simplify the interface for some users.  There can be two different files, corresponding to these two main purposes, listing items to be hidden or disabled.  One kind of file modifies the interface unconditionally during the run of the program; it is specified with the property entry 'DisableOrHideFile' followed by the full path of the file, which can be anywhere.  The other kind of file defines a basic mode for the interface that can be toggled with the Basic Mode command in the Settings menu.  By default, the program will look for such a file, named 'SEMbasicModeItems.txt' in the system directory where the properties and calibration files reside.  The property 'BasicModeDisableHideFile' can be entered with the full path to an alternative file, which can be anywhere and named anything.

Before you add a 'DisableOrHideFile' entry that makes settings unavailable, be sure that the settings files being used have good values for those settings, since it will become impossible for users to fix a bad value.

Each line in one of these files consists of two entries: an initial value of 1 or 2 to indicate whether the item should be disabled or hidden, and a unique identifier for the item.  The first table below lists items for which the identifier is a string that is defined in the program; when using one of these, you need to copy the exact string shown.  However, any item in the program's menus can be hidden simply by entering its numeric ID as the identifier for that item, so the second table below lists these IDs for all menu items.  That table also shows the menu strings; these are not required in the file, but you should copy enough of the string so that you know what the item is afterwards.

These files can also have blank lines and comment lines with a # as the first character.

A file for a Basic mode constructed by Tillman Shaefer is available at http://bio3d.colorado.edu/ftp/SerialEM/Tools/SEMbasicModeItems.txt. This may provide a good starting point for your own customized Basic mode.

Table of Items Defined by Strings

These are items currently eligible to be hidden.  (No disabling has been requested, and it would be more difficult to implement generically than hiding).  If you want to have an item added to this table, contact the SerialEM developers.  To hide or disable an item, you must copy the whole identifier string shown here into your file to use it.  The entries in this table start with '1' if the item can disabled but not hidden, '2' if the item can be hidden but not disabled, or '1 OR 2' if it can both hidden and disabled.  In the latter case, after copying the line, remove the 'OR 2' to disable the item or '1 OR' to hide the item.

The first few lines of this table illustrate some features:

# Must include the group too
# Removes whole line
2 MultishotDlg - Center shots
2 MultishotDlg - Center shot group
# Removes whole line
2 MultishotDlg - Second ring
# A sub-menu item
2 Cal - IS&Stage - Stage Shift
# A main menu item
2 Cal - Mag Energy Shifts
# An entire menu
2 Calibration menu
2 Tilt Series menu
 
# Whole submenus
2 Beam & Spot submenu
2 Pixel Size submenu
2 Focus & Tuning submenu
2 Correlation Filter submenu
2 Special Settings submenu
# In Calibration Focus & Tune submenu
2 Old Coma-Free Alignment submenu
# In Focus & Tune menu
2 Old Coma-free Alignment submenu
2 Specialized Options submenu
2 Nav. Options submenu
 
# Whole control panels
2 Buffer Status panel
2 Buffer Control panel
2 Image Display panel
2 Scope Control panel
2 Tilt panel
 
# Options sections in control panels
2 Buffer Control options
2 Image Display options
2 Scope Status options
2 Tilt panel options
2 Image Align options
2 Low Dose options
2 Montage Control options
2 STEM Control options
2 Filter Control options
2 DE Camera options
 
# Low dose panel
2 LowDoseDlg - Continuous update
# Must include the group too
# Removes whole line
2 LowDoseDlg - Added beam Shift
2 LowDoseDlg - Added beam group
 
# Offsets section: first three will hide it completely
# Removes whole line
2 LowDoseDlg - Offsets View
# Removes whole line
2 LowDoseDlg - Offsets Def spin
2 LowDoseDlg - Offsets line 5
# Otherwise use entries for singel items
2 LowDoseDlg - Offsets group
2 LowDoseDlg - Offsets line 1
2 LowDoseDlg - Offsets line 2
2 LowDoseDlg - Offsets line 3
2 LowDoseDlg - Offsets line 4
2 LowDoseDlg - Offsets Search
2 LowDoseDlg - Offsets Shift label
2 LowDoseDlg - Offsets Set
2 LowDoseDlg - Offsets Zero
2 LowDoseDlg - Offsets Def label
2 LowDoseDlg - Offsets Def value
 
# Image Alignment & Focus panel
# Removes whole line
2 ImageAlignFocus - Align
2 ImageAlignFocus - Clear
2 ImageAlignFocus - To marker
 
# Montage control panel
2 MontControl - Prescan
 
# Filter Control panel   (hiding will leave empty space)
2 FilterControl - TEM screen down
 
# STEM Control panel   (hiding will leave empty space)
2 STEMControl - TEM screen down
 
# Montage Setup Dialog
# Removes whole line
2 MontSetupDlg - Piece size
# Removes whole line
2 MontSetupDlg - Overlap
# Removes whole line
2 MontSetupDlg - Min overlap label
# Someone could get stuck with this
2 MontSetupDlg - Move stage
2 MontSetupDlg - Skip pieces check
2 MontSetupDlg - Skip pieces edit
2 MontSetupDlg - Do full rect
2 MontSetupDlg - Ask about map
2 MontSetupDlg - Use mont-map
2 MontSetupDlg - Use View
2 MontSetupDlg - Use Search
2 MontSetupDlg - Continuous check
2 MontSetupDlg - Continuous edit
2 MontSetupDlg - Turn off drift
2 MontSetupDlg - Use high quality
 
# Imaging State Dialog
2 ImageStateDlg - Add current
2 ImageStateDlg - Add Nav
2 ImageStateDlg - Delete
2 ImageStateDlg - Update
2 ImageStateDlg - Name label
2 ImageStateDlg - Name edit
2 ImageStateDlg - Map acquire
2 ImageStateDlg - Scheduled
2 ImageStateDlg - Restore
2 ImageStateDlg - Forget
 
# Frame File Options Dialog
2 FrameFileOpts - Save MRC
2 FrameFileOpts - Use .mrcs
2 FrameFileOpts - LZW compressed
2 FrameFileOpts - ZIP compressed
# The group box
2 FrameFileOpts - File type
# This is Falcon 4 EER mode
2 FrameFileOpts - One frame/file
2 FrameFileOpts - Frame stack mdoc
2 FrameFileOpts - Save unnormalized
2 FrameFileOpts - No rotation/flip
      

Table of All Menu Items and Their IDs

To hide a menu item not listed above, you can copy the line for that item from this table into your file.  The text after the ID number is optional but will help you identify the entry.

  
FILE MENU
2 32775 Open New
2 32776 Open Old
2 32965 New Montage
2 32778 Montage Setup
2 32779 Close
2 32784 Save A
2 32780 Save Active
2 32805 Overwrite
2 32772 Save Single
2 32781 Set Truncation
2 32926 Set 16-bit Policy
2 32944 Set Signed Policy
2 33289 Skip File Properties Dlg
2 32773 Read
2 32783 Read from Other
2 32806 Read Piece
2 32812 Open Log
2 32813 Save Log
2 32864 Save Log As
2 32950 Read & Append
2 33056 Continuous Save
2 33431 Use Monospaced Font
2 33412 Reset Log Position
2 33181 Open .mdoc for Frames
2 33180 Close Frames .mdoc
  
SETTINGS MENU
2 32795 Open
2 32801 Reload
2 32797 Save
2 32798 Save As
2 32799 Close
2 33307 Discard on Exit
2 32802 Read Defaults
2 32930 Autosave
2 33061 Set Email Address
2 33272 Set a Property
2 33415 Basic Mode
  
CAMERA MENU
2 32786 Parameters
2 32907 Prepare Gain Ref
2 32998 Gain Ref Policy
2 33282 Search
2 32788 View
2 32789 Focus
2 32790 Trial
2 32791 Record
2 32894 Preview
2 32807 Montage
2 32808 Prescan
  
   Correlation Filter submenu
   2 33248 Use Filter Set 2
   2 33249 Use Set 2 in Low Dose
   2 33250 Divide Filter Set 1 by 2
   2 33251 Divide Filter Set 2 by 2
   2 33252 Test Values for Set 1
   2 33253 Test Values for Set 2
   2 33254 Redo Corr when Read
  
2 33044 Set Minimum Counts
2 32794 Stop Acquire
2 33280 Use View for Search
2 33281 No Mont. Map Params
2 32900 Show Gain Ref
2 32901 Show Dark Ref
2 32878 Post-actions
2 32937 Normalize Here
2 32933 Divide 16-bit by 2
2 33407 Set Extra Divisions
2 33408 Return Float Images
2 33073 Interpolate Dark Refs
2 33271 Set Frame Align Lines
  
   Special Settings submenu
   2 33233 No Norm of DS Dose Frac
   2 33333 Always Antialias K2/K3
   2 32897 Set Timing
   2 33197 Set Quality
   2 32942 Set Scanning
   2 33055 Set Drift Interval
   2 32936 Set Corrections
   2 32792 Screen Down
   2 32793 Simulation
  
2 32898 Debug Mode
  
CALIBRATION MENU
   Image & Stage Shift submenu
   2 32804 Image Shift
   2 32874 IS from Scratch
   2 32916 Stage Shift
   2 33153 Whole Image Corr
   2 33159 Set Cycle Lengths
   2 33224 Use Trial Binning
   2 33225 Use Trial Size
   2 32949 List IS Vectors
   2 32953 List Stage Cals
   2 33229 Remove IS Cal
   2 33230 Remove Stage Cal
   2 32980 Mag IS Offsets
   2 32981 EFTEM IS Offset
   2 33099 Set IS Delay Factor
  
   Pixel Size submenu
   2 33053 Find Pixel Size
   2 33054 Try Again with Marker
   2 33115 Set Binned Size
   2 33164 Add n*90 to a Rotation
   2 33076 List Relative Rotations
   2 33193 Catalase Crystal
   2 33216 Mesh for Grid Bars
  
   Focus & Tuning submenu
   2 32814 Autofocus
   2 32848 Set Focus Range
   2 33429 Extended Autofocus
   2 33430 Set Extended Range
   2 32996 Standard Focus
   2 33103 STEM Focus Vs. Z
   2 33214 Base Focus Values
   2 33294 Astigmatism by CTF
   2 33236 Astigmatism by BTID
   2 33241 Setup Astigmatism
   2 33303 Coma vs. Image Shift
  
      Old Coma-Free Alignment sub-submenu
      2 33237 BTID Coma-free Aligment
      2 33240 Setup BTID Coma-free
  
   2 33207 List Calibrations
  
   Beam & Spot submenu
   2 33411 Illuminated Area Limits
   2 32927 Beam Crossover
   2 32865 Beam Intensity
   2 32945 Spot Intensity
   2 32925 Set C2 Factor
   2 32895 Beam Shift
   2 33410 Refine Beam Shift
   2 33122 Alpha Beam Shifts
   2 33217 Spot Beam Shifts
   2 33334 List Calibrations
  
2 33148 Set Aperture Size
2 32924 Electron Dose
2 32946 Purge Old Calibs
2 32915 Distortion
2 32928 Set Overlaps
2 32902 Mag Energy Shifts
2 32910 List Mags
2 32943 Neutral IS Values
2 33215 Restore Neutral IS
2 33075 Stage Stretch
2 33257 High-Defocus Mag
2 33258 List Focus-Mag Cals
2 32935 Camera Timing
2 33114 Quick Flyback Time
2 32954 Shutter Dead Time
2 32815 Administrator
2 32803 Save Calibrations
2 32956 Set Debug Output
  
FOCUS/TUNE MENU
2 32817 Measure Defocus
2 32818 Autofocus
2 32883 Move Focus Center
2 32908 Check Autofocus
2 32821 Report Shift & Drift
2 32912 Report on Existing
2 32970 Show Existing Corr
2 33223 Show Image Stretch
2 32816 Set Target
2 32819 Set Beam Tilt
2 32913 Set Offset
2 32820 Set Threshold
2 33151 Set Tilt Direction
2 33209 Set Min Binning
2 33212 Test Filter Cutoffs
2 32822 Drift Protection
2 33268 Set Absolute Limits
2 33269 Use Absolute Limits
2 33270 Limit Offset Defocus
2 33296 Correct Astigmatism by CTF
2 33298 Coma-free Alignment by CTF
2 33297 Set CTF Acquire Params
2 33302 Set CTF Coma-free Params
2 33275 Beam-tilted FFT Array
2 33238 Correct Astigmatism by BTID
2 33242 Set BTID Astig Beam Tilt
  
   Old Coma-free Alignment submenu
   2 33239 BTID Coma-free Alignment
   2 33243 Set Beam Tilt
   2 33276 Set Iterations
   2 33274 Run Another Iteration
  
2 32938 Reset Defocus
2 32891 Verbose
  
SCRIPT MENU
2 33288 Edit/Run One Line
2 32843 Stop
2 32844 End
2 32845 Resume
2 33000 Toolbar
2 33038 Set Height
2 32846 Controls
2 33401 Load New Package
2 33402 Save Package
2 33403 Save Package As
2 33182 Load Many
2 33235 List Functions
2 33400 List Persistent Vars
2 33284 Clear Persistent Vars
2 33277 Set Indent Size
2 33422 Show Indent Buttons
2 33421 Use Monospaced Font
2 33416 Run at Program Start
2 33417 Run at Program End
2 33306 Open Editors on Start
2 33057 Verbose
  
TASKS MENU
   Eucentricity submenu
   2 32871 Rough Eucentricity
   2 32872 Fine Eucentricity
   2 32873 Both Rough and Fine
   2 32881 Refine & Realign
   2 32932 Set Tilt Axis Offset
   2 33069 Use Trial in LD Refine
   2 33420 Rough Use Search if in LM
   2 33425 Eucentricity by Focus
   2 33426 Calibrate Focus Targets
  
2 32880 Set intensity
2 33177 Set Dose Rate
2 32896 Move beam
2 32982 Center Beam
2 33048 Autocenter Beam
2 33047 Setup Autocenter
2 33094 Walk Up
2 32914 Walkup & Anchor
2 33120 Use View in LD
2 33010 Set Increments
2 33045 Setup Cooker
2 33046 Cook Specimen
2 33063 Assess Angle Range
2 33108 Assess Interset Shifts
2 33110 Revise/Cancel Shifts
2 33095 Reset IS & Realign
2 32939 Set Iteration Limit
2 32940 Use Trial in LD
2 33398 Setup VPP Conditioning
2 33335 Setup Wait for Drift
2 32875 Reverse Tilt
2 33428 Setup Scope Management
2 32892 Verbose
  
   Specialized Options submenu
   2 33206 Disable Dark Trim in Align
   2 33231 Adjust Focus on Probe Mode Change
   2 33278 Normalize All on Mag Change
   2 33419 Turn Off Beam after Long Inactivity
   2 33220 Normalize via View for Autofocus 
   2 33397 Skip Blanking in LD when Screen Up
   2 33433 Keep Focus & Trial at Same Position
   2 33432 Tasks Use View Even if Search Better
   2 33219 Allow Continuous in TS
   2 33190 Skip Beam Shift in TS
   2 33189 Piezo for LD Axis Shift
  
TILT SERIES MENU
2 32879 Setup/Start
2 32890 Terminate
2 32966 Extra Output
2 33003 Batch Policies
2 32999 Reset Pole Angle
2 33245 Run Script in TS 
2 33246 Set Script to Run
2 33185 Call TS Plugins
2 33060 Send Email at End
2 33263 Fixed # of K2/3 Frames
2 33434 Set Bidir Return Delay
2 32884 STOP
2 32885 End Loop
2 32887 Back Up
2 32886 Resume
2 32888 One Loop
2 32889 One Step
2 33232 Save X/Y/Z File
2 33234 Autosave X/Y/Z File
2 32893 Verbose
2 32911 Autosave Log
2 32909 Debug Mode
  
PROCESS MENU
2 32866 Min/Max/Mean
2 32876 Zero-tilt Mean
2 32867 FFT
2 32868 Binned FFT
2 32967 Live FFT
2 33227 Side by Side
2 33259 Automatic Single FFTs
2 33005 Circle on Live FFT
2 33261 Set Defocus for Circles
2 33291 Do CTF Fit on Click
2 33292 Set CTF Fit Options
2 32869 Rotate Left
2 32870 Rotate Right
2 33074 Crop Image
2 33290 Reduce Image
2 33201 Crop & Average
2 33062 Make Color Overlay
2 32955 Show Cross-corr
2 33123 Autocorrelation
2 32903 Fix Dark X-rays
2 32905 Set Dark Criteria
2 32951 Fix Image X-rays
2 32952 Set Image Criteria
  
NAVIGATOR MENU
2 32917 Open
2 32920 Read & Open
2 33194 Merge File
2 33088 Save
2 33089 Save As
2 32921 Close
  
   Montaging & Grids submenu
   2 33090 Setup Corner Montage
   2 33091 Setup Polygon Montage
   2 32931 Setup Full Montage
   2 32995 Set Grid Limits
   2 32948 Setup Super Montage
   2 33016 Polygon Super Montage
   2 33405 Find Holes in Regular Grid
   2 33042 Add Grid of Points
   2 33305 Add Grid Like Last One
   2 33221 Divide Points into Groups
   2 33222 Set Group Radius
   2 33286 Set Multi-shot Parameters
   2 33406 Combine Points for Multi-shots
   2 33285 Show Shots when Show Acquire
   2 33304 Show Whole Area for All Points
   2 33013 Add Circle Polygon
   2 33101 Polygon from Corners
  
   Nav. Options submenu
   2 33267 Set Point Label Threshold
   2 33418 Use Item Labels in Filenames
   2 32929 Autosave Nav File
   2 33264 Write as XML File
   2 32941 Convert Maps to Bytes
   2 32994 Load Maps Unbinned
   2 33279 Use Current LD Params in Realign
   2 33413 Search + and - Scaling in Realign
  
2 33092 Transform Items
2 33040 Undo Transformation
2 32979 Change Registration
2 33071 Align with Rotation
2 32991 Shift to Marker
2 33423 Apply Saved Shift
2 32992 Undo Last Shift
2 33085 New Map from Image
2 33039 Import Map
2 32987 Rotate Map
2 33117 Adjust for Backlash
2 33118 Backlash Settings
2 33064 Open Imaging States 
2 33009 Set Map Acquire State
2 33008 Restore State
2 33086 Acquire at Items
2 33004 End Acquire
2 33043 List Files/Series/States
2 33087 Delete Item
2 32988 Realign to Item
2 33427 Setup Align/Realign
2 33203 Force Center Align
2 33112 Try Scaling in Realign