Updated documentation for 3.1.0

SPIERSalign/docs/requirements.rst

@@ -11,4 +11,4 @@ SPIERSalign has no minimum requirements as such, and will run on most systems; i
 Data
 ----
 
-SPIERSalign works with windows bitmap format files (ending with a .bmp extension), PNGs (.png) and jpegs (.jpg/.jpeg). Files can be either 24-bit RGB or 8-bit greyscale, and of any resolution. The dataset can also comprise images of different resolutions (although this is not recommended). There are no restrictions on filenames: an identifier followed by a three or four digit number (e.g. mydata0001.bmp) is recommended for clarity. Note that the program will order image files alphabetically, and hence that leading zeroes are required on filenames (e.g. image0001.bmp rather than image1.bmp). All images must be placed in a single directory.
+SPIERSalign works with windows bitmap format files (ending with a .bmp extension), PNGs (.png), TIFFs (.tif/.tiff) and jpegs (.jpg/.jpeg). Files can be either 24-bit RGB or 8-bit greyscale, and of any resolution. The dataset can also comprise images of different resolutions (although this is not recommended). There are no restrictions on filenames: an identifier followed by a three or four digit number (e.g. mydata0001.bmp) is recommended for clarity. Note that the program will order image files alphabetically, and hence that leading zeroes are required on filenames (e.g. image0001.bmp rather than image1.bmp). All images must be placed in a single directory.

SPIERSedit/docs/basicconcepts.rst

@@ -73,7 +73,7 @@ rectangle will appear. This is the *threshold image* (see Fig. 2).
 
 .. figure:: _static/figure_1.png
     :align: center
-	
+
     Figure 1. The new dataset window
 
 
@@ -92,8 +92,10 @@ mirrored!
 
 .. figure:: _static/figure_2.png
     :align: center
-
-    Figure 2. The SPIERSedit default window layout
+
+    Figure 2. The SPIERSedit default window layout. Note that the GUI and layout shown corresponds
+    to SPIERS 2.X.X. The GUI for 3.X.X employs a dark theme, and has a slightly modified layout, but
+    all instructions in the documentation applies to 3.X.X.   
 
 Window Layout, Zoom, and Navigation
 -----------------------------------
@@ -110,16 +112,18 @@ shown/hidden using commands in the *Window* Menu, or by using the
 keyboard shorcuts, which are: *F1* - *Main* Toolbox; *F2* - *Slice*
 *selector* panel; *F3* – *Generation* panel; *F4* – *Masks* panel; *F5*
 – *Segments* panel; *F6* – *Curves* panel; *F7* – *Output* panel; *F8* –
-*Histogram* panel; *F9* – *Info* panel.
+*Histogram* panel; *F9* – *Info* panel. An alternative shortcut - shift + control/
+command + the numbers 1-9 - is also available for these panels.
 
 The large initially black box in the centre of the screen is the
 *Threshold image* (see below); this may or may not incorporate scroll
 bars depending on the size of the image relative to the SPIERSedit
-window. To its left is the *Zoom level* slider, and below is the
+window. If scroll bars are present, middle mouse drag translates the image.
+To its left is the *Zoom level* slider, and below is the
 *Position in dataset* slider. The former controls the magnification of
 the images shown; shortcut keys *Q* and *A* also zoom in and out
 respectively, and zoom values can be typed into the associated
-‘spinbox’.
+‘spinbox’. Middle mouse scroll also adjust the zoom.
 
 SPIERSedit only displays one image at a time from the dataset. The ','
 (back, <) and '.' (forward, >) keys are used to move forward or backward
@@ -131,7 +135,8 @@ displays the current dataset, and image file path. The *Slice Selector*
 Panel, if visible, will also show the current file, as moving to a slice
 automatically selects it. Note however that changing selections in this
 panel does not move to a different image, but selects images for various
-operations discussed later.
+operations discussed later. Control + mouse scroll modifies the selected
+slice.
 
 At the top of the window, below the menus, is a permanently visible
 toolbar – this contains buttons for selecting/indicating which of its
@@ -255,7 +260,7 @@ material is present.
 
 .. figure:: _static/figure_3.png
     :align: center
-	
+
     Figure 3. Linear Generation examples. A; source image. B; too dark.(to few white pixels) C; too light (too many white pixels). D; about right.
 
 Generating Multiple Slices
@@ -292,7 +297,7 @@ editing.
 
 .. figure:: _static/figure_4.png
     :align: center
-	
+
     Figure 4. An image requiring editing. Source image is shown on right and thresholded image on left.  A; lighter than normal structure not fully picked out. B; Thin structure not picked out at all. C; lighter area of fossil-fill identified as matrix. D; dark blob in the matrix (noise) identified as fossil (this identified by eye as non-fossil by tracing it through several images, and confirming that it does not attach to the rest of the specimen). E; set of structures appearing a ‘fatter’ than they should and merged into each other. F; darker background material misidentified as fossil. G; edge-padding introduced during alignment misidentified as fossil.
 
 *Figure 4. An image requiring editing*. Source image is shown on right
@@ -353,7 +358,7 @@ Curve, Lock/selection and Mask modes is given later in this document.
 
 .. figure:: _static/figure_5.png
     :align: center
-	
+
     Figure 5. Mode selection toggle buttons.
 
 *Brightness mode:* allows manual cleaning of data by locally adjusting
@@ -371,7 +376,7 @@ material is ‘on’ (e.g. error E in Fig. 4).
 
 .. figure:: _static/figure_6.png
     :align: center
-	
+
     Figure 6. Effects of brightness brush.
 
 The strength of the brightening and darkening effect from a single
@@ -480,4 +485,4 @@ of SPIERSedit read through all these sections, but for those in a hurry
 the most important sections (in no particular order) are *Masks* (which
 allow splitting of a model into colour-coded parts), *Segments* (which
 allow for multiple types of material in a model), and *Output* (which
-covers how to export and view models with multiple masks and segments).
+covers how to export and view models with multiple masks and segments).

SPIERSedit/docs/requirements.rst

@@ -31,15 +31,12 @@ SPIERSedit can work with any dataset consisting of serial ‘slice’
 images, so long as the resolution and scale of each image is the same,
 and no images are missing from the sequence. Datasets should comprise
 registered (aligned) serial images, ideally in uncompressed Windows
-Bitmap (.bmp) format. SPIERSedit can also work with datasets in Portable
-Network Graphic (.png) or JPEG (.jpg) format; these take up less
-hard-disk space, but will normally result in slower processing; JPEG
-datasets will be considerably more compact than Portable Network Graphic
-datasets, but are not recommended as JPEG compression causes artefacts
-which can degrade data and hence final models.
+Bitmap (.bmp) format or Portable Network Graphic (.png). SPIERSedit also supports
+TIIFF (.tif/.tiff) and JPEG (.jpg) format; JPEG datasets are not recommended
+as JPEG compression causes artefacts which can degrade data and hence final models.
 
-*Format*: Images can be 8-bit grayscale (.png, .bmp) or 24-bit colour
-(.bmp, .png, .jpg). Images that lack colour information (e.g. CT data)
+*Format*: Images can be 8-bit grayscale (.png, .bmp, .tiff) or 24-bit colour
+(.bmp, .png, .jpg, .tiff). Images that lack colour information (e.g. CT data)
 should be converted to an 8-bit rather than 24-bit format – you will not
 see a difference visually, but the software will run substantially
 faster.
@@ -62,4 +59,4 @@ loading into SPIERSedit is hence strongly recommended. SPIERSalign can
 be used to perform this croppping, and hence it is normal to pass even
 pre-registered data (e.g. from a CT scanner) through SPIERSalign before
 loading into SPIERSedit. Note that once editing work in SPIERSedit has
-begun it is not possible to re-crop images without all work being lost.
+begun it is not possible to re-crop images without all work being lost.