Version log

0.0.7dev

Thu 1 Jun 17:30:09 BST 2023

  • issue#27 : hkl to shelx
    • script
    • download button test

Thu 1 Jun 10:54:33 BST 2023

  • issue#29:bloch rock
  • enable exp/sim rocking curves option
  • axis option to frame/index/Sw when show rocking curve
  • record rock_frames when simulated experimental frames
  • fix minor bug when switching to structure with no exp data while bloch['u0']=auto
  • fix get_rock_sim callback when switching to rock mode with no simulation data
  • changed the info.graphs structure
  • get automatic reflection selection in rock mode when refreshing
  • clear flag in update_refl callback when clearing table

0.0.6

Wed 31 May 22:10:13 BST 2023

  • issue#29 : bloch rock
  • change axis from Sw to Frame

Wed 31 May 12:34:51 BST 2023

  • created file static/views/main.html for main layout
  • template dependent variables present in header and footer still in templates/main.html
  • minor bug fix

Wed 31 May 11:16:35 BST 2023

  • issue#24: simulated integration
  • button to integrate at all thicknesses
  • show integrated reflections across thickness

Wed 31 May 09:38:41 BST 2023

  • minor fix in pixel range

Tue 30 May 13:23:20 BST 2023

  • issue#29 :bloch rock
  • modified modes['u'] modes into single,rock,lacbed with corresponding buttons
  • created modes['u0'] modes as auto,move,edit with corresponding buttons when modes['u']=='single'
  • removed modes['manual']
  • changed set_u_mode into set_mode(key,val) which dispatches to set_u_mode(val) and set_u0_mode(val)
  • first and last frame automatic retrieval

Tue 30 May 10:43:38 BST 2023

  • added fast forward and fast backward to exp data frame
  • fix minor bug when new session

Fri 26 May 14:11:29 BST 2023

  • issue#36 : diff pattern axis
  • Enable passing from pixels to rec angstrom
  • change yaxis orientation up/down

Thu 25 May 21:19:49 BST 2023

  • issue#33 : show Nmax and dmin

Thu 25 May 20:45:34 BST 2023

  • issue#23 : import exp data auto orientation
  • works for dials(spot location wrong though)
  • wavelength retrieval
  • fix xds file should be a .HKL extension
  • issue#35 refactor import dataset
  • dials and xds have a base class
  • pets has a common interface but does not inherit base class yet

Thu 25 May 04:23:52 BST 2023

  • issue#23 : auto orientation
  • works for pets
  • works for xds
  • issue#35 refactor import dataset
  • unifying the data process interface with info : npx,rpl,cen
  • function hkl_to_pixels(hkl,frame) to obtain pixel locations from miller indices
  • partially removed the omega feature
  • modified pets so that its uvw is already correctly oriented and should not need a negative sign in edly
  • fix bug frames panel not available when only the processed data exist
  • fix error pets_file when no .pts present
  • implemented a,w,s,d hotkeys for moving in rotation tweaking mode
  • added some basic Mathjax ready startup stuffs

Tue 23 May 17:21:28 BST 2023

  • issue#37 : space group info
  • display space group, lattice system and number of atoms.
  • provide link to ucl chem space group info page
  • obtained a dictionary to pass from space group it number to hm symbol and vice versa

Tue 23 May 01:25:24 BST 2023

  • issue#29 : rocking curve
  • active simulation updated properly when passing from rock to other mode
  • u_sim orientation permanently above the mode options
  • rock solve button with the normal bloch solve button
  • solve rock available again when changing simulation parameters
  • rock solve should always complete properly now

Mon 22 May 18:15:19 BST 2023

  • moved omega parameter into frames panel
  • bundled omega and offset into a settings expand menu.

Mon 22 May 17:11:53 BST 2023

  • issue#29 : rocking curve
  • put the u_sim orientation permanently on top of solve panel
  • fixed bugs in updating u for sim and frames

Fri 19 May 16:30:12 BST 2023

  • issue#34 : bloch frames
  • put the u_frame in the frames panel
  • cosmetic :(color,padding,etc...)
  • fixed some bugs when session cookies are deleted

Fri 19 May 10:54:33 BST 2023

  • issue#33 : pass from resolution to index
  • issue#30 : updating graph even when deleting reflections

Thu 18 May 15:19:40 BST 2023

  • issue#29 : rocking curve
  • automatically solve for rocking curve
  • fixed bugs solve rock
  • fixed wrong sign pinned orientation value
  • fixed bug manual and single modes
  • changed init bug setTimeOut with interval cancelled only after $scope.init=true

Thu 18 May 11:50:13 BST 2023

  • issue#28 : tweak orientation

Thu 18 May 11:15:52 BST 2023

  • issue#21 : resolution rings bugs
  • bug with hiding data when no rings present
  • bug hiding rings does not always work for all rings
  • setting rings spacing to 0 result in no rings at all now

Wed 17 May 17:18:48 BST 2023

  • might have fixed initialization error bug with setTimeOut

Wed 17 May 16:16:34 BST 2023

  • issue#30 reflections :
  • clear button
  • put the automatically selected reflections in the table
  • automatic refresh option
  • try fixing bug key error data['bloch'] at refresh(due to init occasionally called after init_bloch_panel )

Wed 17 May 13:15:26 BST 2023

  • issue#29 : Bloch experimental rocking curves
  • fixed switching u modes bug

Tue 16 May 19:12:01 BST 2023

  • issue#35 refactor import dataset :
  • datasets loaded in in_out.pyff
  • issue#31 :
  • enable reading exp frames without cif_file
  • disable solvers if cif_file not provided
  • modified naming for nb_frames
  • added cbf reader
  • cleaned code

Tue 16 May 13:32:48 BST 2023

  • issue#34 :
  • fixed bloch frame overflow (pets.uvw does not contain the 5 last tiff images )
  • bloch not recalculated if the frame actually did not change
  • heatmap option only shown when in frames mode
  • bloch does not recalculate when switching mode if frame has not changed (repaced ng-switch directive with ng-show and moved controllers div outside of the ng-show directive so initialization does not happen every time the div is shown)

Mon 15 May 20:11:43 BST 2023

  • issue#34 : implemented canvas
  • fixed bug with chemical formula was not fully working
  • fixed bug with frame overflow and frame numbering (biotin starts at 0, glycine starts at 1)

0.0.5

(Fri 28 Apr 17:44:15 BST 2023)

  • remove (0,0,0) dials exp reflections
  • fix omega bug when using pred_info with dials

(Thu 28 Jul 15:33:06 BST 2022)

  • enabled display pattern in pixels (stable for all dials/pets/no_data)
  • enable to choose between pixel and rec space

(Tue 19 Jul 18:19:22 BST 2022)

  • implement tab index for frames
  • moved bloch related calls to bloch.py
  • reactivated modes.single (other modes are still buggy)

(Tue 19 Jul 17:08:56 BST 2022)

  • changed felix path to dedicated directory
  • added more attempts in load_b0
  • added lacbed option only if available in felix
  • retractable frame offset
  • biotin dataset imported with pets

Fri 15 Jul 20:19:58 BST 2022

  • fixed bug reload image when changing frames
  • fixed bug reload frames when switching to frames
  • fixed init bug for structures with no available images
  • fixed bug with update_visible
  • fixed omega update bug
  • dials import functionalities
  • fixed bloch init session data
  • image toggle reload button

(Tue Jul 12 15:50:46 2022 +0100)

  • added felix support
  • lacbed patterns

0.0.4

Mon 23 May 10:46:46 BST 2022

  • Vga and Sw legendonly at start
  • lock u switching to glycine
  • created set_viewer with url parameters
  • introduced server dependent home url
  • added version number

0.0.3

issue#18 (Sat 21 May 17:44:05 BST 2022)

  • Use gemmi
  • use resolution dmin instead of Nmax
  • changed import style when doing new structure(pdb saved to file now)
  • create object at init_mol and only update it after

issue#12 FELIX option (Fri 20 May 13:24:16 BST 2022)

  • enable solve from Felix with bloch_state recording
  • felix widget with nbeams parameter
  • added rings step
  • changed cif file handling due to crystals lib pbs
  • minor change on get_frame
  • left/right for large thickness stepping
  • automatic reflection expand on select and thickness on solved

0.0.2

Thu 19 May 12:08:35 BST 2022

  • fixed bug updating thickness for rocking curve simu
  • updating rocking curves thickness
  • fixed graph rock session saved
  • fixed occasional bug at end of rock simulations

Wed 18 May 15:01:58 BST 2022

  • fixed bug not re updating when changing structure
  • fixed bug re initializing all arguments when changing structure
  • scattering factors viewer
  • added solver state bloch_state
  • added resolution rings
  • graph fig2 saved in session

Tue 17 May 17:40:15 BST 2022

  • added username info

Tue 17 May 11:19:21 BST 2022

  • Solve bloch state created to prevent solving when already being solved
  • interval rock not working on VM : get('/') fixed
  • rocking curve error : thick taken from session['bloch']
  • rocking curve orientations error : needed calling get_uvw_cont
  • issue#15 : help menu links

(Tue 26 Apr 09:51:41 BST 2022)

  • hide error after closing dialog
  • import cif
  • added links
  • fixed frame enter issue due to ng-if

(Tue 26 Apr 00:58:23 BST 2022)

  • projects (new, other projects, ...)
  • links : (theory,documentation,tests)
  • help
  • pets orientation vector u
  • y range goes from xm to -xm
  • set_intensities with FELIX convention
  • import crambin

issue#16 miller indices table (Fri 22 Apr 20:26:20 BST 2022)

  • highlight on hover
  • removed update when changing analysis mode

issue#11 rocking curve (Fri 22 Apr 16:03:47 BST 2022)

  • use arrows or select frame
  • set u from frame
  • I_pets updated from current frame in rock_mode
  • max res input
  • added footer copyright
  • expandable structure parameters
  • added info for miller table
  • created tabs for modes['analysis'] preparing for multislice

(Thu 21 Apr 16:24:22 BST 2022)

  • rock graph only available in rock mode
  • update reflection table in session

0.0.1

issue#9 ( Thu 21 Apr 16:24:22 BST 2022)

  • graph selector
  • plotly menu for the curves to show
  • use b0_path to fix beam_vs_thickness update in rock mode
  • show_u includes all orientation in auto mode (very slow)
  • click enter on rock frame for specifying input
  • change graphs layout to align dropdown menu nicely

issue#6 (Tue 19 Apr 15:42:37 BST 2022)

  • beam selection from plotly
  • add rpx,rpy,Ipets data to the plotly graph
  • show miller indices when hovering over data points
  • add a callback which adds/removes in a javascript array the selected hkl
  • use and show proper markers
  • add a background color (light blue) to the graph
  • persistent xylims
  • persistent data visibility
  • adding MathJax dependency
  • added structure info in crys
  • bloch solver layout with expandable parameters
  • added rotation parameter omega
  • added selected beams to rocking curve and thickness dep
  • bug fix when updating frame orientation vector

issue#8 (Mon 11 Apr 16:53:08 BST 2022)

  • Rocking curve
  • compute and display rocking curve in side figure
  • add panel for rocking curve parameters
  • show computation evolution
  • go through rocking patterns
  • toggle rocking/overlay images
  • add figure for showing 3d orientation
  • created in_out.py
  • added gg-icons.css
  • use modes['u'] to str (move,edit,rock)

issue#7 (Fri 8 Apr 12:38:20 BST 2022)

  • display b0.beam_vs_thickness in either another window or aside of analysis
  • toggle button for dual view
  • updates on press enter for thickness, range, u inputs
  • arrows for changing thickness and dthick
  • grouped show_molecule,analysis_mode... into session['modes'][mode] for better control over saving session state and toggles
  • split solve_bloch into update_bloch and bloch_fig for better update of update_thick

issue#10 (Thu 7 Apr 14:46:11 BST 2022)

  • created rotation_mode
  • bw_app.py:solve_bloch split into 2 functions to accommodate for bloch_rotation
  • pets data loaded when sessions are created
  • arrows can be used to change orientation when the rotation panel is focused
  • library bloch.py modified to include I key even when not solved.

issue#5 (Sun 3 Apr 19:12:17 BST 2022)

  • add all parameters inputs to Bloch solver
  • import processed data
  • update u,keV

issue#3 (Sat 2 Apr 11:41:22 BST 2022)

  • button JSmol to visualise the structure
  • buttons (with popups):
    • upload : exp tiffs data
    • upload : simulated data
    • upload : pets/dials processed data

issue#4 (Thu 31 Mar 15:58:14 BST 2022)

  • simu vs exp avec refl side by side
  • toggle button to pass to single analysis mode
  • added cif file to bloch solver
  • split update_zmax for exp/sim frame
  • added project/molecule row in html
  • added default data for test structure
    • to install it : cd static/data/; ln -s ../../test test
  • clear a session : rm -rf static/data/tmp/<session_id>
  • initial bloch param setup

issue#2 ('Tue Mar 29 18:56:50 2022')

  • resave png image when updating zmax
  • server must now be run with ./serve.py (bw_app registered with Blueprint)
  • introduced sessions to be cleaner
  • split in app.js update into update_bloch and update_img

issue#1

  • visualisation de df_G.[I,Swa,Vga]