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Tina6/tina-tools/ChangeLog

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  1 Project     : tina-tools
  2 Description : tinatool application code
  3 ---------------------------------------
  4 
  5 ChangeLog
  6 ---------
  7 
  8 This is the changelog file for the tinatools application (tina-tools).  Make an entry
  9 in this file for each change to the code stored in the central repository on server6,
 10 copying the format of previous entries.  Entries should:
 11 
 12  - be made in reverse chronological order i.e. most recent at the top;
 13 
 14  - include details of files modified and added, details of the nature and purpose of
 15    the change, the platform on which you are working, and any other details which
 16    other developers should be aware of;
 17 
 18  - tagged with an ID (incremented from the last).
 19 
 20 The build number in the configure.ac file in the tina-tools directory should also be 
 21 changed to the ID of the entry.
 22 
 23 ----------------------------------------------------------------------------------
 24 ID:17 nat 30/1/2015 (linux 2.6.22)
 25 
 26         .pointer to int casts fixed to remove compile errors, tested by JD
 27         .histogram plotting modified to allow float values
 28 M drawPlot_procs.c
 29 M drawPaint_imrect.c  
 30 M drawTv_show.c      
 31 M wdgtsGtk_tw_svalue.c
 32 M tlbaseDisp_tool.c  
 33 M wdgtsNull_tw_notebook.c
 34 
 35 ------------------------------------------------------------------------------------
 36 ID:16 hr 12/3/2013 (linux 2.6.22)
 37 
 38         . Resolved few bugs in Imcalc Tool and Histogram Tool.
 39 
 40 M tlbaseImc_tool.c
 41 M drawPlot_graph.c
 42 
 43 ------------------------------------------------------------------------------------
 44 ID:15 hr 17/10/2012 (linux 2.6.22)
 45 
 46         . Modified wdgts/null/Makefile.am and gphx/null/Makefile.am to reflect 
 47           the addition of new null files and to make them compatible with tina6.
 48 
 49 M Makefile.am
 50 
 51 ------------------------------------------------------------------------------------
 52 ID:14 hr 17/10/2012 (linux 2.6.22)
 53 
 54         . Changed the build/version number to [6.0rcbuild010].
 55 
 56 ------------------------------------------------------------------------------------
 57 ID:13 hr 2/8/2012 (linux 2.6.22)
 58 
 59         . Added null versions of the new files and routines in wdgts/null.
 60 
 61 A wdgtsNull_tw_notebook.c
 62 A wdgtsNull_tw_notebook.h
 63 
 64 M gphxNull_cmap.c
 65 M gphxNull_cmap.h
 66 
 67 M wdgtsNull_tw_scan_files.c
 68 M wdgtsNull_tw_scan_files.h
 69 
 70 ------------------------------------------------------------------------------------
 71 ID:12 hr 31/7/2012 (linux 2.6.22)
 72 
 73         . Added null versions of the new files in wdgts/null.
 74 
 75 A wdgtsNull_tw_colourbutton.c
 76 A wdgtsNull_tw_colourbutton.h
 77 
 78 A wdgtsGtk_tw_curve.c
 79 A wdgtsGtk_tw_curve.h
 80 
 81 A wdgtsNull_tw_keyvalue.c
 82 A wdgtsNull_tw_keyvalue.h
 83 
 84 A wdgtsNull_tw_progressbar.c
 85 A wdgtsNull_tw_progressbar.h
 86 
 87 M wdgts_NullDef.h
 88 
 89 ------------------------------------------------------------------------------------
 90 ID:11 hr 27/7/2012 (linux 2.6.22)
 91 
 92         . Added the null version of the missing gphx/gdk2 routines (tv_screen_rgb_set;
 93           tv_screen_col_image; rgb_from_long_uint) in gphx/null.
 94 
 95 M gphxNull_draw.c
 96 M gphxNull_draw.h
 97 M gphxNull_color.c
 98 M gphxNull_color.h
 99 
100 M gphx_NullDef.h
101 
102 ------------------------------------------------------------------------------------
103 ID:10 hr 26/7/2012 (linux 2.6.22)
104 
105         . Changed the build/version number to [6.0rcbuild009].
106 
107 ------------------------------------------------------------------------------------
108 ID:9 hr 19/6/2012 (linux 2.6.22)
109 
110         . Functionality added to pgh location to allow image reprojection.
111 
112 M tlbaseHist_tool.c
113 M tlbaseHist_tool.h
114 M tlbaseImc_tool.c
115 M tlbaseImc_tool.h
116 
117 M tlmedAnl_mouse.c
118 M tlmedAnl_mouse.h
119 M tlmedAnl_tool.c
120 M tlmedAnl_tool.h
121 
122 --------------------------------------------------------------------------------------
123 ID:8 pab 13/2/2012 (linux 2.6.22)
124 
125         . Small bug fixes.
126 
127         . Modified the signal handler for key value entry to prevent focus moving 
128           around the dialog box if e.g. the arrow keys are entered.
129 
130 M wdgtsGtk_tw_keyvalue.c
131 M wdgtsGtk_tw_keyvalue.h
132 
133         . Removed the set deletable call, since this does not exist in the Gtk library
134           version on the Suns in the NiAC lab.  Instead, a signal handler function 
135           will print a warning and prevent deletion of the progress bar.
136 
137 M wdgtsGtk_tw_progressbar.c
138 M wdgtsGtk_tw_progressbar.h
139 
140         . Fixed a histogram scaling bug in the histogram tool.
141 
142 M tlbaseHist_tool.c
143 M tlbaseHist_tool.h
144 
145         . Removed an irrelevant warning message related to macro files that contain
146           the macro file append button
147 
148 M tlbaseMcr_tool.c
149 M tlbaseMcr_tool.h
150 
151 
152 --------------------------------------------------------------------------------------
153 ID:7 pab 9/12/2011 (linux 2.6.22)
154 
155         . Changes to support Manual Landmark tool v1.6.
156 
157         . Fixed a bug in the tv and display tool code, where the pointers to the
158           canvas and owner were cast to int then back to pointers.  This causes
159           problems when the memory pointed to is above the 32-bit address limit, 
160           since the conversion loses half of the pointer.  
161 
162 M tlbaseDisp_display.c
163 M tlbaseDisp_display.h
164 M tlbaseDisp_tool.c
165 M wdgtsGtk_tw_screen.c
166 M wdgtsGtk_tw_screen.h
167 
168 
169         . The old sequence loader had the capability to downsample across the 
170           inter-slice direction by simply skipping slices; this is controlled by the 
171           stride parameter in the interface.  Added an option that allows downsampling 
172           by loading all slices and then averaging in the inter-slice direction to 
173           produce the final sequence.  This reduces the image noise and results in 
174           improvements to the accuracy of the Manual Landmarking tool.  However, it 
175           could potentially cause problems for other code if, for example, some 
176           variable parameter of the acquisition was extracted from the DICOM header 
177           and used in subseqent analysis, and it was not valid to apply linear 
178           averaing to this parameter.  Therefore, the inter-slice smoothing is 
179           controlled by a choice list in the interface, and the default setting is "Off".
180 
181 M tlbaseSeq_io.c
182 M tlbaseSeq_io.h
183 M tlbaseSeq_tool.c
184 
185         . Fixed a small error in the in-line documentation.
186 
187 M wdgtsGtk_tw_curve.c
188 
189         . Added a progress bar widget; see the documentation in the c file for 
190           instructions on how to use it.
191 
192 A wdgtsGtk_tw_progressbar.c
193 A wdgtsGtk_tw_progressbar.h
194 M wdgts_GtkPro.h
195 M wdgtsPro.h
196 
197 
198 --------------------------------------------------------------------------------------
199 ID 6 nat 7/7/2011 (linux/solaris)
200 
201         . New functionality added to corner tool and calib tool to support manual
202           calibration and computation of 3D positions. New functionality added to 
203           edge_tool to allow the selection of a faster (simple) edge link scheme, 
204           suitable for algorithms which require raw edge data.
205         
206 M tlvisCalib_tool.c  
207 M tlvisCnr_pick.c    
208 M tlvisCnr_tool.c    
209 M tlvisEdge_tool.c
210 M tlmedCort_tool.c
211 M tlmedCoreg_view.c
212 M tlbaseHist_tool.c
213 M drawPaint_pick2.c
214 
215 --------------------------------------------------------------------------------------
216 ID:5 pab 14/12/2010 (linux 2.6.22)
217 
218 
219         . Added checks for NULL tvs, tv_screens and masks; the lack of these was 
220           causing a crash when a function tried to draw a graph in the Imcalc 
221           graph Tv whilst the Imcalc tool was open (so that the Tv existed) but 
222           no Tv tool had been installed on the Imcalc graph Tv (so that the 
223           Tv_screen did not exist).
224 
225 M drawTv_mask.c
226 
227         . Modified a comment regarding the above issue.
228 
229 M gphxGdk_mask.c
230 
231         . Fixed a couple of missing header files.
232 
233 M gphxGdk_color.c
234 M gphxGdk_color.h
235 
236         . In previous versions the tv_picture structure contained a GdkImage.  This 
237           had several drawbacks: GdkImages are server-side objects, so manipulating 
238           individual pixels is slow; somewhere between Gtk 2.8 and Gtk 2.20, the 
239           (deprecated) function gdk_image_get ceased to work properly, leading to 
240           graphical corruption when Tvs with a backdraw function tried to repaint 
241           the stored background, or when the dump tool was used (the two places that 
242           this structure is used in TINA).  Therefore, this structure has been changed 
243           to use a GdkPixbuf instead, which is a client-side object and solves these 
244           problems. Gtk 3 will eliminate all GdkImages, GdkPixmaps  and GdkBitmaps in 
245           favour of using Cairo to do all drawing operations, eliminating all of these 
246           considerations completely.
247 
248 M gphx_GdkDef.h
249 M gphxGdk_draw.c
250 M gphxGdk_dump.c
251 M gphxGdk_epsf_dump.c
252 M gphxGdk_tiff_dump.c
253 M gphxGdk_picture.c
254 
255 
256 --------------------------------------------------------------------------------------
257 ID:4 pab 23/06/2010 (linux 2.6.22)
258 
259         . Swapped the definition of the mouse buttons in ZOOM4 mode, so that rotation 
260           is on the left button and scaling is on the right.
261 
262 M drawTv_activity.c
263 M drawTv_zoom.c
264 M drawTv_zoom.h
265 
266 
267         . Added the capability to assign keyboard shortcuts to Tvs.  This works in a 
268           similar way to the mouse functionality; when a key is pressed with the focus 
269           on a Tv tool, a Gtk event is triggered that calls a function assigned to the 
270           Tv.  The list of Gdk codes for each key is contained in gphx_GdkDef.h (and, 
271           if a new graphics library interface is ever written, will have to be 
272           replaced with the relevant list for that graphics library), so that the key 
273           codes returned by Gdk can be compared to the definitions in this list.  The 
274           function that receives the key press can be assigned in the make function 
275           for a Tv using tv_set_keyboard_func(tv, function).
276 
277 M draw_TvDef.h
278 A drawTv_keyboard.c
279 A drawTv_keyboard.h
280 M draw_TvPro.h
281 M drawTv_tv.c
282 M gphx_GdkDef.h
283 M wdgts_GtkPro.h
284 M wdgtsGtk_tw_screen.c
285 
286         . Added a special version of the text entry widget that displays a text 
287           description of the key that has been pressed, rather than the text normally 
288           generated by that key.  This can be used to build dialog boxes that allow 
289           the user to reassign keyboard shortcuts in Tv tools.
290 
291 A wdgtsGtk_tw_keyvalue.c
292 A wdgtsGtk_tw_keyvalue.h
293 
294         . Prevent the buttons in TINA from having keyboard focus; this interferes 
295           with the operation of the dialog box used to assign keys to Tv tool keyboard 
296           shortcuts e.g. the user may want to assign the return key as a shortcut, but 
297           if buttons in the dialog box can have keyboard focus then pressing the 
298           return key will also activate the button that currently has focus.
299 
300 M wdgtsGtk_tw_button.c
301 
302           Fixed a missing include file bug for rgb_from_long_uint.
303 
304 M gphxGdk_mask.c
305 
306         . Attempted to sort out the operation of the scan function (file browser) 
307           re: filename extensions.  TINA has a problem with this in that, when the 
308           filebrowser widget is used to select a file to load, the extension is 
309           automatically stripped from the filename.  Most of the loading functions 
310           then add the expected extension; however, not all of them do this and the 
311           extension may be non-standard e.g. we assume that DICOM has no extension, 
312           but sometimes .dcm is used.  This causes a problem for the user who selects 
313           a file and presses load, only to be told that the file dows not exist 
314           because they have not re-added the extension.  In order to sort this out, 
315           two new filebrowser functions have been added: scan_files_with_extension 
316           and scan_files_without_extension, the first of which leaves the extension 
317           in place and the second of which removes it.  The scan_files function is 
318           now a wrapper allowing the default behaviour to be changed; it currently 
319           uses scan_files_with_extension.  All tools that will automatically add the 
320           extension (mono tool, roi tool and stereo tool and sequence tool) have been 
321           modified so that they strip the existing extension from the filename 
322           returned from the filebrowser, so that their previous behaviour is 
323           maintainned.  Note that this does not fix the problem (on loading DICOM 
324           files with the .dcm extension the user will still have to re-add the 
325           extension to the filename; we can't change that without potentially breaking 
326           old macro files), but moves us in the right direction; in future programmers 
327           will have to consider what to do with the extension, rather than ignoring 
328           the problem.
329 
330         . Also changed the size of the string used to store the directory and filenames 
331           of the input file in tlbaseSeq_roitool.c, from 64 characters to MAXPATHLEN.
332 
333         . Also fixed the sequence tool casting functions, so that the sequence is not 
334           cast to binary when the user runs off of the end of it uing the increment or 
335           decrement frame buttons or the "jump to" button.
336 
337         . Also, the tlbaseSeq_tool.c file contains a commented-out example of how to 
338           do millisecond-accurate timing tests (useful for performance evalulation).
339 
340 M wdgtsGtk_tw_scan_files.c
341 M wdgtsGtk_tw_scan_files.h
342 M tlbaseMono_tool.c
343 M tlbaseSeq_roitool.c
344 M tlbaseSeq_tool.c
345 M tlbaseSter_tool.c
346 
347         . Added a warning that TINA cannot output DICOM or NEMA files when the user tries 
348           to save a sequence in this format.
349 
350 M tlbaseSeq_io.c
351 
352         . Added the abilit to store a curve contained in a curve widget as a set of 
353           control points, via a structure in wdgtsDef.h, so that it can be replicated 
354           exactly (the Gtk functions only allow the curve to be stored as a vector of 
355           points of a user-defined length; they do not allow easy access to the control 
356           points).  The tw_curve_apply function in wdgtsGtk_tw_curve allows a forced 
357           call to the apply button e.g. if the curve information is loaded from a file.
358 
359 M wdgtsDef.h
360 M wdgtsGtk_tw_curve.c
361 M wdgtsGtk_tw_curve.h
362 
363         . Modified the button that spawns a colour selection dialog box so that an 
364           initial colour can be passed to it if a previous selection has been made 
365           (rather than starting with white), and added a reset function so that the 
366           colour swatch on the button can be set from within TINA.
367 
368 M wdgtsGtk_tw_colourbutton.c
369 M wdgtsGtk_tw_colourbutton.h
370 
371         . Additional prototypes for several of the updates listed above
372 
373 wdgtsPro.h
374 
375 
376 --------------------------------------------------------------------------------------
377 ID:3 pab 12/03/2010 (linux 2.6.22)
378 
379         . Modifications to the libraries to support the new manual landmarking tool,
380           developed as part of the collaborative project with the Max Planck Institute
381           for Evolutionary Biology.
382 
383         . Added two new functions (tv_col_image2 and tv_col_imrect2) that allow the 
384           display of full colour images in TINA Tv tools, by bypassing the TINA 
385           colourmap functionality and using GTK RGB drawing functions directly. NOTE:
386           this is a first step; all drawing should eventually migrate towards using 
387           these functions, allowing all of the colourmap code to be deprecated.
388 
389 M drawPaint_imrect.c
390 M drawPaint_imrect.h
391 
392         . Added a new choice of mouse functionality for 3D Tv's (ZOOM4), with fully 3D
393           rotations (ZOOM3 uses tv_rot on the middle mouse button, which rotates the 
394           2D image) and does not draw in overlay mode.  This is required by the manual
395           landmarking tool, which draws in a different way to the other 3D Tv's in 
396           TINA (the 3D rendering is done by an external library, producing a 2D image 
397           for display, but the 3D mouse functionality is done by TINA).  However, 
398           since overlay mode is not used, ZOOM4 requires that double-buffering is used 
399           on the Tv to ensure that the display is flushed during mouse manipulations.
400 
401 M draw_TvDef.h
402 M drawTv_zoom.c
403 M drawTv_zoom.h
404 
405         . Added Tv activity messages for the ZOOM3 and ZOOM4 cases.
406 
407 M drawTv_activity.c
408 M drawTv_activity.h
409 
410         . Added a function (tv_color_set_rgb) to set the colour of a Tv using RGB
411           values directly, bypassing the TINA colourmap functionality.
412 
413 M drawTv_props.c
414 M drawTv_props.h
415 
416         . Added a new function (tv_screen_rgb_set) that sets the forground colour
417           of a Tv using RGB values directly, bypassing the TINA colourmap 
418           functionality.
419 
420 M gphxGdk_color.c
421 M gphxGdk_color.h
422 
423         . Added a new function (tv_screen_col_image) that draws a colour image to a 
424           Tv screen using GTK's RGB drawing functions, bypassing the TINA colourmap 
425           functionality completely.
426 
427 M gphxGdk_draw.c
428 M gphxGdk_draw.h
429 
430         . New button widget that spawns a GTK colour selection dialog
431 
432 A wdgtsGtk_tw_colourbutton.c
433 A wdgtsGtk_tw_colourbutton.h
434 
435         . New widget based on the GTK curve widget, allowing freeform definition of 
436           lookup tables.
437 
438 A wdgtsGtk_tw_curve.c
439 A wdgtsGtk_tw_curve.h
440 
441         . Small modification to the macro reader function, allowing longer lines to 
442           support the new curve widget.
443 
444 M wdgtsGtk_tw_command.c
445 
446         . Fixed both s(global/value) reset functions: gtk_entry_set_text requires a 
447           const string.
448 
449 M wdgtsGtk_tw_sglobal.c
450 M wdgtsGtk_tw_svalue.c
451 
452         . Included the new ZOOM4 mode as a case in make_movie_proc.
453 
454 M tlbaseView_tool.c
455 
456         . Added a new colour Tv to the colour tool, which displays a full-colour 
457           version of the image currently loaded into the tool using the new colour
458           image drawing functionality.
459 
460 M tlbaseColour_tool.c
461 M tlbaseColour_view.c
462 M tlbaseColour_view.h
463 
464         . Modification to the sequence tool to allow images to be downsampled on loading
465           (for the case where the sequence is too large to fit in available memory).  A
466           new field (downsample) has been added to the sequence structure to indicate
467           this.
468 
469 M tlbaseSeq_io.c
470 M tlbaseSeq_io.h
471 M tlbaseSeq_tool.c
472 
473 --------------------------------------------------------------------------------------
474 ID:2 pab 06/11/2009 (linux 2.6.22)
475 
476         . Fixed a small memory leak in tv_screen_set_linewidth and 
477           tv_screen_set_linestyle, where the GdkGCValues structures were allocated 
478           but never freed.
479 
480 M gphxGdk_props.c
481 
482 --------------------------------------------------------------------------------------
483 ID:1 pab 04/11/2009 (linux 2.6.22)
484 
485         . First RC of TINA 6
486           Changes compared to TINA 5:
487 
488             - extensive rewrite of build system.
489             - all widget library interfaces except GTK+ 2 removed.
490 
491 EOF-----------------------------------------------------------------------------------
492 

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