diff --git a/afniandafni/gui_guide/afni_gui_datamode.rst b/afniandafni/gui_guide/afni_gui_datamode.rst index ba1b4ed..bb45467 100644 --- a/afniandafni/gui_guide/afni_gui_datamode.rst +++ b/afniandafni/gui_guide/afni_gui_datamode.rst @@ -282,10 +282,10 @@ Define Datamode **note to staff: button help in the gui needs to be updated** .. list-table:: - :width: 100% + :widths: 65 35 :align: center :header-rows: 0 - + * - * ``Voxel Coords?`` will toggle the crosshair location from *mm* (the default) to voxel indexes. * ``Show Hints?`` will turn off (on is the default) the popup @@ -300,12 +300,15 @@ Define Datamode controller window :ref:`(See here.)`. * ``Edit 1DChain`` and ``Edit 2DChain`` open controllers for - applying functions to your data. **note to staff: I have no - idea what these do...** + applying functions or combinations of functions to your data. + :ref:`See here` for info on + some of the transformations for 1DChain in the graph window. + :ref:`See here` for info on + some of the transformations for 2DChain in the image window. * ``Save Layout`` - + - .. image:: media/datamode_Misc_popup.png - :width: 70% + :width: 100% :align: right - .. image:: media/datamode_Misc.png diff --git a/afniandafni/gui_guide/afni_gui_image.rst b/afniandafni/gui_guide/afni_gui_image.rst index d7be672..00e252d 100644 --- a/afniandafni/gui_guide/afni_gui_image.rst +++ b/afniandafni/gui_guide/afni_gui_image.rst @@ -191,7 +191,7 @@ Image Window * Smallest-to-largest display range is selected from the ``Disp`` control panel. :ref:`(see here)`, or from the right click hidden popup menu - :ref:`(see below)`. + :ref:`(see here)`. * Scroll-wheel in the intensity bar changes contrast. * ALT (``⌘`` on macOS) plus scroll-wheel in intensity bar changes brightness. @@ -220,7 +220,7 @@ Image Window * ``Swap`` swaps top of intensity bar with bottom. (handy to see things like the bounding box or abnormalities depending on the type of data). This is similar to the ``Invert?`` button - :ref:`(see below)`. + :ref:`(see here)`. * ``Norm`` returns the intensity bar to normal (after you mess it up). * ``c`` controls contrast. ``b`` controls brightness. @@ -667,9 +667,9 @@ It pops up its own control window and most controls change image immediately. * ``Maximum`` = largest value in the slab. * ``Mean`` = average value in the slab. * ``Median`` = median value in the slab. - * ``OSfilt`` = xxx. - * ``Extreme`` = value farthest from the median. - * ``MAD`` = Mean absolute deviation. + * ``OSfilt`` = Order Statistics filter. The weighted sum of neighbors. + * ``Extreme`` = alue farthest from the median. + * ``MAD`` = Mean Absolute Deviation. * ``AdptMean`` = estimator of the mean. * ``Slab +-`` selects the number of slices around the current view to @@ -704,10 +704,12 @@ It pops up its own control window and most controls change image immediately. - Extreme - MAD - AdptMean + - * - .. image:: media/image_window_Disp_menu_project_OSfilt.png - .. image:: media/image_window_Disp_menu_project_extreme.png - .. image:: media/image_window_Disp_menu_project_MAD.png - .. image:: media/image_window_Disp_menu_project_AdptMean.png + - .. image:: media/image_window_Disp_menu_project_blank.png - .. image:: media/image_window_Disp_menu_project.png :width: 100% @@ -719,55 +721,200 @@ It pops up its own control window and most controls change image immediately. :widths: 80 20 :header-rows: 1 - * - :ref:`The Rest` + * - :ref:`Transforms` - * - * ``Tran 0D`` lets you transform voxel values before display. ``Log10`` and ``SSqrt`` are useful for images with extreme values. - * ``Tran 2D`` provides some 2D image filters for the underlay only. + + .. list-table:: + :width: 100% + :align: center + :header-rows: 1 + + * - None + - Log10 + - SSqrt + - Abs + * - .. image:: media/image_window_Disp_tran_none.png + - .. image:: media/image_window_Disp_tran_0D_log10.png + - .. image:: media/image_window_Disp_tran_0D_SSqrt.png + - .. image:: media/image_window_Disp_tran_0D_ABS.png + + * ``Tran 2D`` provides some 2D image filters for the underlay as a whole. ``Median 9`` smoothing can be useful for printing images. - * ``RowGraphs`` are plots of the underlay (grayscale) image intensity + + .. list-table:: + :width: 100% + :align: center + :header-rows: 1 + + * - Median9 + - Winsor9 + - OSfilt9 + - Median21 + - Winsor21 + * - .. image:: media/image_window_Disp_tran_2D_Median9.png + - .. image:: media/image_window_Disp_tran_2D_Winsor9.png + - .. image:: media/image_window_Disp_tran_2D_OSfilt9.png + - .. image:: media/image_window_Disp_tran_2D_Median21.png + - .. image:: media/image_window_Disp_tran_2D_Winsor21.png + + .. list-table:: + :width: 100% + :align: center + :header-rows: 1 + + * - AdptMean21 + - abs[FFT2D] + - arg[FFT2D] + - Sharpness + - 2DChain (combos) + * - .. image:: media/image_window_Disp_tran_2D_AdptMean21.png + - .. image:: media/image_window_Disp_tran_2D_absfft2d.png + - .. image:: media/image_window_Disp_tran_2D_argfft2d.png + - .. image:: media/image_window_Disp_tran_2D_sharpness.png + - .. image:: media/image_window_Disp_menu_project_blank.png + + * 0D and 2D transformations can be combined for further effects. + * :ref:`See here` for info on how to use the + 2DChain option. + + - .. image:: media/image_window_Disp_menu_tran.png + :width: 100% + :align: left + + +.. _gui_guide_image_window_RowGraphs: + +.. list-table:: + :widths: 80 20 + :header-rows: 1 + + * - :ref:`Row Graphs` + - + * - * ``RowGraphs`` are plots of the underlay (grayscale) image intensity as x vs. y graphs. .. list-table:: - :width: 100% + :width: 90% :align: center :header-rows: 0 * - .. image:: media/image_window_Disp_RowGraphs.png :width: 100% - * Each graph is from one displayed horizontal row of - the image. - * The bottom rowgraph is from the image row under the crosshairs. - * Upper rowgraphs are from higher image rows. - * Image transformation functions and image rotation/flips will affect - the rowgraphs as well as the image display. - * The color marker indicates the crosshair focus point and can be - hidden with the ``No Overlay`` button. - * If you want columns, flip the image with ``CCW 90``. - - * ``Surfgraph`` lets you graph the voxel values in a surface graph. + * Each graph is from one displayed horizontal row of + the image. + * The bottom row graph is from the image row under the crosshairs. + * Upper row graphs are from higher image rows. + * Image transformation functions and image rotation/flips will affect + the row graphs as well as the image display. + * The color marker indicates the crosshair focus point and can be + hidden with the ``No Overlay`` button. + * If you want columns, flip the image with ``CCW 90``. + :ref:`(see here)` + * The number of graphs ranges from 0 to 9. + + - .. image:: media/image_window_Disp_menu_RowGraphs.png + :width: 100% + :align: left + +.. _gui_guide_image_window_surfgraph: + +.. list-table:: + :widths: 80 20 + :header-rows: 1 + + * - :ref:`Surf Graphs` + - + * - * ``Surfgraph`` lets you graph the voxel values in a surface graph. + * These are a wire mesh plot of the underlay (grayscale) image + intensity vs x and y. + * Options ``No``, ``Yes``, and ``Inv``. + * These plots can be saved from the viewer window. However, they + look much better if you maximize the window and take a screen shot. + * Use the arrows in the ``SurfGraph`` window to rotate the view point. + * Use the middle button between the arrows to reset the viewpoint to + the default orientation. + * The plotting routine may produce some erroneous vertical lines on + occasion. + * The color "UK Flag" marker indicates the crosshair focus point. It + is drawn on top of the surface at the end. So it is always visible + even if it should be hidden behind the surface. It shines through + no matter what. + * The color marker can be turned off with the "No Overlay" button. .. list-table:: :width: 100% :align: center - :header-rows: 0 - + :header-rows: 1 + + * - Standard Surf Graph * - .. image:: media/image_window_Disp_SurfGraph.png :width: 100% - * Extra imaging processing filters are provided at the bottom. These + .. list-table:: + :width: 100% + :align: center + :header-rows: 1 + + * - Inverse Surf Graph + * - .. image:: media/image_window_Disp_SurfGraph_inv.png + :width: 100% + + - .. image:: media/image_window_Disp_menu_SurfGraph.png + :width: 100% + :align: left + + +.. _gui_guide_image_window_filters: + +.. list-table:: + :widths: 80 20 + :header-rows: 1 + + * - :ref:`Filters` + - + * - * Extra imaging processing filters are provided at the bottom. These options have extra parameters adjustable in the intensity bar popup - window. :ref:`(see below)` + window. :ref:`(see here)` - * ``Flatten`` "flattens" the histogram of the image similar effect as + * ``Flatten`` "Flattens" the histogram of the image similar effect as adjusting the brightness and contrast manually. - * ``Sharpen`` is sometimes useful for deblurring images. + * ``Sharpen`` applies a sharpening filter to the background. This is + sometimes useful for deblurring images. * ``Edge Detect`` applies a Sobel edge detection filter. This is useful as the underlay for checking alignment. * ``VG paint`` applies a "painting" effect to the image just for fun. - - - .. image:: media/image_window_Disp_menu.png + * You can use any combination of these filters and the + :ref:`transformations` + to create some interesting images. + + .. list-table:: + :width: 100% + :align: center + :header-rows: 1 + + * - None + - Flatten + - Sharpen + * - .. image:: media/image_window_Disp_filters_none.png + - .. image:: media/image_window_Disp_filters_flatten.png + - .. image:: media/image_window_Disp_filters_sharpen.png + + .. list-table:: + :width: 100% + :align: center + :header-rows: 1 + + * - Edge Detect + - VG Paint + - Combo + * - .. image:: media/image_window_Disp_filters_edge.png + - .. image:: media/image_window_Disp_filters_paint.png + - .. image:: media/image_window_Disp_filters_flat_sharp_paint.png + + - .. image:: media/image_window_Disp_menu_filters.png :width: 100% :align: left @@ -783,8 +930,6 @@ Intensity Bar Hidden Popup :align: center * - :ref:`Vertical Intensity Bar Popup` - - - * - AFNI GUI: Image Window Intensity Bar Popup * - .. image:: media/image_window_IntensityBar_Popup.png :width: 75% :align: center @@ -841,6 +986,10 @@ only appear in the image window and do not change the data set on disk. - .. image:: media/image_window_IntensityBar_Popup_disp_range_200_4111_hist.png :width: 100% + * To get those histogram plots, go to ``Define Datamode ->`` then + ``Plugins`` then ``Histogram`` and select your underlay as the + source. + - .. image:: media/image_window_IntensityBar_Popup_disp_range.png :width: 100% :align: right @@ -937,7 +1086,7 @@ only appear in the image window and do not change the data set on disk. `here `_. * This function is the same as the ``Swap`` button except that the image is automasked and the background is not inverted. - :ref:`(see above)`. + :ref:`(see here)`. * The program `fat_proc_imit2w_from_t1w `_ does something similar but saves an output data set. @@ -969,8 +1118,34 @@ only appear in the image window and do not change the data set on disk. * - :ref:`Choose Flatten Range ` - - * - * ``Choose Flatten Range`` - * + * - * ``Choose Flatten Range`` allows you to adjust the "flattening" range + of the ``Flatten`` filter that you can select from the ``Disp`` menu. + :ref:`(see here)` + * The default is something reasonable. You can return to the default + by deleting the numbers entered and clicking ``Set``. + + .. list-table:: + :width: 100% + :align: center + :header-rows: 0 + + * - Selecting ``Choose Flatten Range`` opens a dialog box like + this (but with no numbers entered). + - .. image:: media/image_window_IntensityBar_Popup_flatten_dialog.png + :width: 80% + :align: center + + .. list-table:: + :width: 100% + :align: center + :header-rows: 1 + + * - None + - Default + - 10 to 50 + * - .. image:: media/image_window_IntensityBar_Popup_flatten_none.png + - .. image:: media/image_window_IntensityBar_Popup_flatten_default.png + - .. image:: media/image_window_IntensityBar_Popup_flatten_10_50.png - .. image:: media/image_window_IntensityBar_Popup_flatten.png :width: 100% @@ -985,8 +1160,35 @@ only appear in the image window and do not change the data set on disk. * - :ref:`Choose Sharpen factor ` - - * - * ``Choose Sharpen factor`` - * + * - * ``Choose Sharpen factor`` allows you to adjust the amount of + "sharpening" that the ``Sharpen`` filter applies when you select it + from the ``Disp`` menu. + :ref:`(see here)` + * The default amount is 6. You can choose an integer from 1 to 9. + Lower numbers equal less sharpening. + + .. list-table:: + :width: 100% + :align: center + :header-rows: 0 + + * - Selecting ``Choose Sharpen factor`` opens this dialog box with + the default value of 6 selected. + - .. image:: media/image_window_IntensityBar_Popup_sharpen_dialog.png + :width: 80% + :align: center + + .. list-table:: + :width: 100% + :align: center + :header-rows: 1 + + * - None + - 6 (default) + - 9 + * - .. image:: media/image_window_IntensityBar_Popup_sharpen_none.png + - .. image:: media/image_window_IntensityBar_Popup_sharpen_default.png + - .. image:: media/image_window_IntensityBar_Popup_sharpen_9.png - .. image:: media/image_window_IntensityBar_Popup_sharpen.png :width: 100% @@ -1002,8 +1204,35 @@ only appear in the image window and do not change the data set on disk. * - :ref:`Choose VG factor ` - - * - * ``VG_factor`` - * + * - * ``VG_factor`` allows you to adjust the amount of the painting effect + that the ``VG paint`` filter applies when you select it + from the ``Disp`` menu. + :ref:`(see here)` + * The default amount is 2. You can choose an integer from 1 to 9. + Higher numbers look more abstract. + + .. list-table:: + :width: 100% + :align: center + :header-rows: 0 + + * - Selecting ``Choose VG factor`` opens this dialog box with + the default value of 2 selected. + - .. image:: media/image_window_IntensityBar_Popup_VG_dialog.png + :width: 80% + :align: center + + .. list-table:: + :width: 100% + :align: center + :header-rows: 1 + + * - None + - 2 (default) + - 9 + * - .. image:: media/image_window_IntensityBar_Popup_sharpen_none.png + - .. image:: media/image_window_IntensityBar_Popup_VG_2.png + - .. image:: media/image_window_IntensityBar_Popup_VG_9.png - .. image:: media/image_window_IntensityBar_Popup_VG_factor.png :width: 100% @@ -1019,8 +1248,24 @@ only appear in the image window and do not change the data set on disk. * - :ref:`Crop Autocenter? ` - - * - * ``crop_autocenter`` - * + * - * ``Crop Autocenter?`` will automatically re-center the cropping + sub-window (if cropping is active) around the crosshair position + (as far as possible). + * This is useful if you want to move around easily after you crop + for looking at images zoomed in. + * This is toggle on/off with off selected by default. + + .. list-table:: + :width: 100% + :align: center + :header-rows: 1 + + * - Autocenter Off + - Autocenter On + * - .. image:: media/image_window_IntensityBar_Popup_crop_autocenter_off.gif + :width: 70% + - .. image:: media/image_window_IntensityBar_Popup_crop_autocenter_on.gif + :width: 70% - .. image:: media/image_window_IntensityBar_Popup_crop_autocenter.png :width: 100% @@ -1035,8 +1280,29 @@ only appear in the image window and do not change the data set on disk. * - :ref:`Image Global Range ` - - * - * ``global_range`` - * + * - * ``Image Global Range`` determines the source of the values from + which the viewer determines the range for display. + * ``Slice`` is the default option which calculates the range from the + individual slice visible in the viewer. + * ``Volume`` uses the range of values from the entire volume. For + multi volume datasets, the range is calculated from the volume + currently selected. + * ``Dataset`` uses the range of values from the entire dataset for + multi volume data sets like functional data. For single volume + datasets like anatomical images, ``Dataset`` and ``Volume`` use the + same range. + + .. list-table:: + :width: 100% + :align: center + :header-rows: 1 + + * - Slice + - Volume + - Dataset + * - .. image:: media/image_window_IntensityBar_Popup_global_range_slice.png + - .. image:: media/image_window_IntensityBar_Popup_global_range_volume.png + - .. image:: media/image_window_IntensityBar_Popup_global_range_dataset.png - .. image:: media/image_window_IntensityBar_Popup_global_range.png :width: 100% @@ -1052,8 +1318,9 @@ only appear in the image window and do not change the data set on disk. * - :ref:`Plot Overlay Plots ` - - * - * ``plot_overlay`` - * + * - * ``Plot Overlay Plots`` is on by default. + * Among other things, controls overlay of cortical surface geometry + sent to AFNI from the SUMA program. - .. image:: media/image_window_IntensityBar_Popup_plot_overlay.png :width: 100% @@ -1069,8 +1336,34 @@ only appear in the image window and do not change the data set on disk. * - :ref:`Display Graymap Plot ` - - * - * ``display_graymap`` - * + * - * ``Display Graymap Plot`` pops up a graymap-versus-data value plot. + * There is a ``save image to file`` button that does what it says. + * If you move a slice a red histogram plot will be overlaid. + * The y axis is gray level (usually 0 to 255). + * The x axis spans the range of the data that is shown. If you have + 2%-to-98% selected (default), the x axis will not include data + above or below that range. If you change the range from the ``Disp`` + menu :ref:`(see here)` or with the + ``Choose Display Range`` button + :ref:`(see here)`, + the x axis will reflect that change. + * The black curve will shift as you change the contrast and brightness + with the ``c`` and ``b`` buttons + :ref:`(see here)` + or using the mouse click and drag method over the image + :ref:`(see here)`. + + .. list-table:: + :width: 100% + :align: center + :header-rows: 1 + + * - Gray Map + - With Histogram + - Curve Shifted + * - .. image:: media/image_window_IntensityBar_Popup_graymap.png + - .. image:: media/image_window_IntensityBar_Popup_graymap_hist.png + - .. image:: media/image_window_IntensityBar_Popup_graymap_shift.png - .. image:: media/image_window_IntensityBar_Popup_display_graymap.png :width: 100% @@ -1086,9 +1379,34 @@ only appear in the image window and do not change the data set on disk. * - :ref:`Label, Size, Label Append String ` - - * - * ``Label`` - * ``Size`` - * ``Label Append String`` + * - * ``Label`` will allow you to display the location of the slice you are + viewing in mm and direction (superior, inferior, etc.). + + * The example below has the slice at 13.68 mm superior. The label is + the z direction because you are viewing the x and y in the axial + image window. Other views will show the appropriate labeling. + * The drop down menu will give you the options for the placement of + the label in relation to the image window. Default is ``Off``, + but the options include all four corners and the top and bottom + centered left to right. + + * ``Size`` lets you choose the size of the label from ``Tiny`` to + ``Enormous``. The default is ``Medium``. + * ``Label Append String`` adds some text to the end of the label. You + need to add a space at the beginning if you want to separate it from + the original label. + + .. list-table:: + :width: 90% + :align: center + :header-rows: 1 + + * - Medium upper left + - Huge + - Huge with custom text + * - .. image:: media/image_window_IntensityBar_Popup_label_default.png + - .. image:: media/image_window_IntensityBar_Popup_label_huge.png + - .. image:: media/image_window_IntensityBar_Popup_label_append.png - .. image:: media/image_window_IntensityBar_Popup_label.png :width: 100% @@ -1101,11 +1419,22 @@ only appear in the image window and do not change the data set on disk. :widths: 80 20 :header-rows: 1 - * - :ref:`Tick Div., Tick Size - ` + * - :ref:`Ticks` - - * - * ``Tick Div.`` - * ``Tick Size`` + * - * ``Tick Div.`` add ticks to the border of the image window. You can + choose from 0 to 21 equal divisions separated by ticks. + * ``Tick Size`` defines the length of the ticks from the border toward + the inside of the image window. 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