diff --git a/docs/guides/connectivity.md b/docs/guides/connectivity.md index 96eddbf..4f440f3 100644 --- a/docs/guides/connectivity.md +++ b/docs/guides/connectivity.md @@ -1,7 +1,7 @@ # Connectivity files The horizontal grids used by E3SM's atmosphere component EAM, and sometimes the -land component ELM as well, are cubed spheres. Since these are unstructed +land component ELM as well, are cubed spheres. Since these are unstructured grids from ParaView's perspective, QuickView needs to know how to map data to the globe. Therefore, for each simulation data file, a "connectivity file" needs to be provided. @@ -19,7 +19,7 @@ Future versions of QuickView will also support the cubed-sphere meshes used by EAM's dynamical core, i.e., the `ne*np4` grids (also referred to as "native grids" or "GLL grids"). -## Connecitivity file download +## Connectivity file download A collection of connectivity files can be found on [Zenodo](https://doi.org/10.5281/zenodo.16908566). The archive is diff --git a/docs/guides/install_and_launch.md b/docs/guides/install_and_launch.md index 7d3acc0..8d25a84 100644 --- a/docs/guides/install_and_launch.md +++ b/docs/guides/install_and_launch.md @@ -95,7 +95,7 @@ quickcompare -p 0 After some seconds, the Terminal window should indicate that the app has loaded various plugins, and then provide an URL similar to `http://localhost:50329/` (your actual number will likely be different). -**Enter the URL into a web brower** to access the graphical UL. +**Enter the URL into a web browser** to access the graphical UL. :::tip Tip: First execution on macOS diff --git a/docs/guides/quickview/file_selection.md b/docs/guides/quickview/file_selection.md index 68b5ebf..e38a1b2 100644 --- a/docs/guides/quickview/file_selection.md +++ b/docs/guides/quickview/file_selection.md @@ -20,7 +20,7 @@ from the file system. The user can single-click a file name and then click the "simulation" or "connectivity" button in the bottom-left corner to clarify file type. -Alternatively, if a filename starts with "connecitivity", then +Alternatively, if a filename starts with "connectivity", then the user can **double-click** the file to have it automatically recognized as a connectivity file. Double-clicking a filename not starting with "connectivity" makes diff --git a/docs/guides/quickview/index.md b/docs/guides/quickview/index.md index 10b6e55..3ac6679 100644 --- a/docs/guides/quickview/index.md +++ b/docs/guides/quickview/index.md @@ -55,10 +55,10 @@ The lead developer of QuickView version 2 is [Sebastien Jourdain](https://www.kitware.com/sebastien-jourdain/) at [Kitware](https://www.kitware.com/). Other key contributors include +Berk Geveci, Dan Lipsa, Patrick O'Leary and Will Dunklin at [Kitware](https://www.kitware.com/) +and Hui Wan and Kai Zhang at [Pacific Northwest National Laboratory](https://www.pnnl.gov/atmospheric-climate-and-earth-sciences-division). -and Berk Geveci, Dan Lipsa, Patrick O'Leary and Will Dunklin -at [Kitware](https://www.kitware.com/). QuickView is a product of an interdisciplinary collaboration supported by the U.S. Department of Energy Office of Science’s diff --git a/docs/guides/quickview/individual_views.md b/docs/guides/quickview/individual_views.md index 62cbda7..b76ecef 100644 --- a/docs/guides/quickview/individual_views.md +++ b/docs/guides/quickview/individual_views.md @@ -1,7 +1,7 @@ ![pop-up panel](./screenshots/single_view_pop-up_panel.png){ width="60%", align=right } -# Custimizing Individual Views +# Customizing Individual Views Each view in the viewport (i.e., each contour plot shown on a global or regional map) can be customized individually by clicking the associated colorbar. @@ -31,12 +31,30 @@ using a fuzzy search on their names. The x icon clears the filter. The second icon in the top-left corner is a toggle for inverting and resetting the sequence of colors. -## Linear and symmetric logarithmic scales {#linear-and-log-scales} +## Linear vs. logarithmic scales {#linear-and-log-scales} -![linear and log](./screenshots/linear_log_icons.png){ width="12%", align=right } +![linear and log](./screenshots/linear_log_icons.png){ width="16%", align=right } -## Automatic and fixed data ranges +QuickView supports both linear and logarithmic color scaling to facilitate the inspection of variables that span multiple orders of magnitude. +- By default, a **linear scale** is used, indicated by a staircase-style icon in the pop-up panel. + +- A click on the staircase icon changes the scaling to **logarithmic** to enhance the visibility of variations across multiple orders of magnitude. + +- Because standard logarithmic scaling is only defined for positive values, QuickView also provides a **symmetric logarithmic (“symlog”)** scale, which accommodates negative values and zero. The symlog scale behaves linearly in a small region around zero and logarithmically away from zero, enabling consistent visualization of fields that include both positive and negative values. + +## Continuous vs. discrete colormaps + +![linear and log](./screenshots/continuous_and_discrete_colormap_icons.png){ width="12%", align=right } + +QuickView supports both continuous and discrete colormaps, which can be toggled using the corresponding icon in the pop-up panel. A continuous colormap maps data values smoothly along a color gradient, so each value is represented by a unique color. In contrast, a discrete colormap groups values into a finite number of color bins, assigning the same color to all values within each bin . + +When a discrete colormap is selected, a text box allows the user to specify the number of colors. + +- With a linear scale, this value is interpreted as the number of colors between two neighboring (automatically determined) colorbar ticks. +- With a logarithmic scale, it instead specifies the number of colors per order of magnitude. + +## Automatic vs. fixed data ranges By default, QuickView automatically fits the selected colormap over the entire range of values of the current variable in the current data slice. diff --git a/docs/guides/quickview/miscellaneous.md b/docs/guides/quickview/miscellaneous.md index 9a43e17..86e0b16 100644 --- a/docs/guides/quickview/miscellaneous.md +++ b/docs/guides/quickview/miscellaneous.md @@ -1,6 +1,6 @@ # Miscellaneous Features -This page summarizes several addtional convenient features in QuickView. +This page summarizes several additional convenient features in QuickView. ## Choosing map projection and extent @@ -51,7 +51,7 @@ or animations for presentations and manuscripts, etc.: After the scan is finished, a file `quickview-animation.zip` gets downloaded to the local computer. This file is a zipped folder that may contain multiple files. -Note: as of version 2.6.0, the animation export downloads +Note: as of version 2.6.1, the animation export downloads images of individual frames to the local computer, and the user needs to use a tool to combine the images into an animation (or animations). Direct download of animation files will be provided soon. diff --git a/docs/guides/quickview/screenshots/animation_control_panel_and_menu.png b/docs/guides/quickview/screenshots/animation_control_panel_and_menu.png index 32aa3e8..34c6e26 100644 Binary files a/docs/guides/quickview/screenshots/animation_control_panel_and_menu.png and b/docs/guides/quickview/screenshots/animation_control_panel_and_menu.png differ diff --git a/docs/guides/quickview/screenshots/animation_download.png b/docs/guides/quickview/screenshots/animation_download.png index 8b4bf0a..32cab0d 100644 Binary files a/docs/guides/quickview/screenshots/animation_download.png and b/docs/guides/quickview/screenshots/animation_download.png differ diff --git a/docs/guides/quickview/screenshots/auto_or_fixed_ranges.png b/docs/guides/quickview/screenshots/auto_or_fixed_ranges.png index a1a8721..e14c951 100644 Binary files a/docs/guides/quickview/screenshots/auto_or_fixed_ranges.png and 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b/docs/guides/quickview/screenshots/fixed_and_auto_range_icons.png differ diff --git a/docs/guides/quickview/screenshots/invert_color_icons.png b/docs/guides/quickview/screenshots/invert_color_icons.png index 5cde668..d0e1440 100644 Binary files a/docs/guides/quickview/screenshots/invert_color_icons.png and b/docs/guides/quickview/screenshots/invert_color_icons.png differ diff --git a/docs/guides/quickview/screenshots/latlon_sliders.png b/docs/guides/quickview/screenshots/latlon_sliders.png index 9cdbb8f..0a3e178 100644 Binary files a/docs/guides/quickview/screenshots/latlon_sliders.png and b/docs/guides/quickview/screenshots/latlon_sliders.png differ diff --git a/docs/guides/quickview/screenshots/linear_log_icons.png b/docs/guides/quickview/screenshots/linear_log_icons.png index 958e6b9..f15ae0e 100644 Binary files a/docs/guides/quickview/screenshots/linear_log_icons.png and b/docs/guides/quickview/screenshots/linear_log_icons.png differ diff --git a/docs/guides/quickview/screenshots/quickview-state_animation_download.json b/docs/guides/quickview/screenshots/quickview-state_animation_download.json new file mode 100644 index 0000000..71d938b --- /dev/null +++ b/docs/guides/quickview/screenshots/quickview-state_animation_download.json @@ -0,0 +1,149 @@ +{ + "origin": { + "user": "huiwan", + "created": "2026-04-29 15:22:02.256346", + "comment": "" + }, + "files": { + "simulation": "/global/cfs/cdirs/m4359/www/huiwan/vis/202601_group_compare/amicphys_r8_prog.eam.h0.2010_2019.ANN.nc", + "connectivity": "/global/cfs/cdirs/m4359/www/huiwan/vis/202601_group_compare/connectivity_ne30pg2_TEMPEST.scrip.nc" + }, + "variables-selection": [ + "AODALL", + "AODBC", + "num_a1", + "num_a2" + ], + "layout": { + "aspect-ratio": 0.5, + "grouped": false, + "active": "auto_layout", + "tools": [ + "adjust-databounds" + ], + "help": false + }, + "data-selection": { + "crop_longitude": [ + -180, + 180 + ], + "crop_latitude": [ + -90, + 90 + ], + "projection": [ + "Mollweide" + ], + "animation_track": "lev", + "lev_idx": 0 + }, + "views": [ + { + "type": [ + "time", + "ncol" + ], + "name": "AODALL", + "config": { + "preset": "BuGnYl", + "invert": false, + "color_blind": false, + "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, + "order": 1, + "size": 6, + "offset": 0, + "break_row": false, + "override_range": false, + "color_range": [ + 0.01264046598225832, + 1.01161527633667 + ], + "color_value_min": "0.01264046598225832", + "color_value_max": "1.01161527633667" + } + }, + { + "type": [ + "time", + "ncol" + ], + "name": "AODBC", + "config": { + "preset": "BuGnYl", + "invert": false, + "color_blind": false, + "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, + "order": 2, + "size": 6, + "offset": 0, + "break_row": false, + "override_range": false, + "color_range": [ + 0.0006716852076351643, + 0.08890804648399353 + ], + "color_value_min": "0.0006716852076351643", + "color_value_max": "0.08890804648399353" + } + }, + { + "type": [ + "time", + "lev", + "ncol" + ], + "name": "num_a1", + "config": { + "preset": "BuGnYl", + "invert": false, + "color_blind": false, + "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, + "order": 3, + "size": 6, + "offset": 0, + "break_row": false, + "override_range": false, + "color_range": [ + 37851584.0, + 432790592.0 + ], + "color_value_min": "37851584.0", + "color_value_max": "432790592.0" + } + }, + { + "type": [ + "time", + "lev", + "ncol" + ], + "name": "num_a2", + "config": { + "preset": "BuGnYl", + "invert": false, + "color_blind": false, + "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, + "order": 4, + "size": 6, + "offset": 0, + "break_row": false, + "override_range": false, + "color_range": [ + 89625480.0, + 12674042880.0 + ], + "color_value_min": "89625480.0", + "color_value_max": "12674042880.0" + } + } + ] +} \ No newline at end of file diff --git a/docs/guides/quickview/screenshots/quickview-state_latlon_sliders.json b/docs/guides/quickview/screenshots/quickview-state_latlon_sliders.json new file mode 100644 index 0000000..dea23b0 --- /dev/null +++ b/docs/guides/quickview/screenshots/quickview-state_latlon_sliders.json @@ -0,0 +1,149 @@ +{ + "origin": { + "user": "huiwan", + "created": "2026-04-29 15:25:40.465295", + "comment": "" + }, + "files": { + "simulation": "/global/cfs/cdirs/m4359/www/huiwan/vis/202601_group_compare/amicphys_r8_prog.eam.h0.2010_2019.ANN.nc", + "connectivity": "/global/cfs/cdirs/m4359/www/huiwan/vis/202601_group_compare/connectivity_ne30pg2_TEMPEST.scrip.nc" + }, + "variables-selection": [ + "AODALL", + "AODBC", + "num_a1", + "num_a2" + ], + "layout": { + "aspect-ratio": 0.5, + "grouped": false, + "active": "auto_layout", + "tools": [ + "adjust-databounds" + ], + "help": false + }, + "data-selection": { + "crop_longitude": [ + -29, + 150 + ], + "crop_latitude": [ + 1, + 90 + ], + "projection": [ + "Robinson" + ], + "animation_track": "lev", + "lev_idx": 0 + }, + "views": [ + { + "type": [ + "time", + "ncol" + ], + "name": "AODALL", + "config": { + "preset": "BuGnYl", + "invert": false, + "color_blind": false, + "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, + "order": 1, + "size": 6, + "offset": 0, + "break_row": false, + "override_range": false, + "color_range": [ + 0.042987335473299026, + 1.01161527633667 + ], + "color_value_min": "0.042987335473299026", + "color_value_max": "1.01161527633667" + } + }, + { + "type": [ + "time", + "ncol" + ], + "name": "AODBC", + "config": { + "preset": "BuGnYl", + "invert": false, + "color_blind": false, + "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, + "order": 2, + "size": 6, + "offset": 0, + "break_row": false, + "override_range": false, + "color_range": [ + 0.001972629688680172, + 0.08890804648399353 + ], + "color_value_min": "0.001972629688680172", + "color_value_max": "0.08890804648399353" + } + }, + { + "type": [ + "time", + "lev", + "ncol" + ], + "name": "num_a1", + "config": { + "preset": "BuGnYl", + "invert": false, + "color_blind": false, + "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, + "order": 3, + "size": 6, + "offset": 0, + "break_row": false, + "override_range": false, + "color_range": [ + 89570888.0, + 432790592.0 + ], + "color_value_min": "89570888.0", + "color_value_max": "432790592.0" + } + }, + { + "type": [ + "time", + "lev", + "ncol" + ], + "name": "num_a2", + "config": { + "preset": "BuGnYl", + "invert": false, + "color_blind": false, + "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, + "order": 4, + "size": 6, + "offset": 0, + "break_row": false, + "override_range": false, + "color_range": [ + 90726912.0, + 963400576.0 + ], + "color_value_min": "90726912.0", + "color_value_max": "963400576.0" + } + } + ] +} \ No newline at end of file diff --git a/docs/guides/quickview/screenshots/quickview-state_quickview_ui.json b/docs/guides/quickview/screenshots/quickview-state_quickview_ui.json new file mode 100644 index 0000000..f9d1bb4 --- /dev/null +++ b/docs/guides/quickview/screenshots/quickview-state_quickview_ui.json @@ -0,0 +1,154 @@ +{ + "origin": { + "user": "huiwan", + "created": "2026-04-29 15:45:55.249432", + "comment": "" + }, + "files": { + "simulation": "/global/cfs/cdirs/m4359/www/huiwan/vis/202508_EAM_QuickView_test_data/large/EAMv2_ne120pg2_spinup.eam.h0.nc", + "connectivity": "/global/cfs/cdirs/m4359/www/huiwan/vis/202508_EAM_QuickView_test_data/connectivity/connectivity_ne120pg2_TEMPEST.scrip.nc" + }, + "variables-selection": [ + "T", + "Q", + "CCN3", + "CLDLOW" + ], + "layout": { + "aspect-ratio": 0.45, + "grouped": false, + "active": "auto_layout", + "tools": [ + "select-fields", + "select-slice-time", + "animation-controls", + "adjust-layout", + "adjust-databounds" + ], + "help": false + }, + "data-selection": { + "crop_longitude": [ + -180, + 180 + ], + "crop_latitude": [ + -90, + 90 + ], + "projection": [ + "Robinson" + ], + "animation_track": "lev", + "lev_idx": 51 + }, + "views": [ + { + "type": [ + "time", + "lev", + "ncol" + ], + "name": "T", + "config": { + "preset": "Yellow - Gray - Blue", + "invert": true, + "color_blind": false, + "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, + "order": 7, + "size": 6, + "offset": 0, + "break_row": false, + "override_range": true, + "color_range": [ + 220.0, + 285.0 + ], + "color_value_min": "220", + "color_value_max": "285" + } + }, + { + "type": [ + "time", + "lev", + "ncol" + ], + "name": "Q", + "config": { + "preset": "batlow", + "invert": false, + "color_blind": false, + "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, + "order": 5, + "size": 6, + "offset": 0, + "break_row": false, + "override_range": true, + "color_range": [ + 0.0, + 0.008 + ], + "color_value_min": "0", + "color_value_max": "0.008" + } + }, + { + "type": [ + "time", + "lev", + "ncol" + ], + "name": "CCN3", + "config": { + "preset": "Rainbow Desaturated", + "invert": false, + "color_blind": false, + "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, + "order": 3, + "size": 6, + "offset": 0, + "break_row": false, + "override_range": true, + "color_range": [ + 0.0, + 260.0 + ], + "color_value_min": "0", + "color_value_max": "260" + } + }, + { + "type": [ + "time", + "ncol" + ], + "name": "CLDLOW", + "config": { + "preset": "Grayscale", + "invert": false, + "color_blind": false, + "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, + "order": 2, + "size": 6, + "offset": 0, + "break_row": false, + "override_range": true, + "color_range": [ + 0.0, + 0.88 + ], + "color_value_min": "0.0", + "color_value_max": "0.88" + } + } + ] +} \ No newline at end of file diff --git a/docs/guides/quickview/screenshots/quickview-state_slice_selection_panel.json b/docs/guides/quickview/screenshots/quickview-state_slice_selection_panel.json index 6cdf7fb..1f156f4 100644 --- a/docs/guides/quickview/screenshots/quickview-state_slice_selection_panel.json +++ b/docs/guides/quickview/screenshots/quickview-state_slice_selection_panel.json @@ -1,8 +1,8 @@ { "origin": { "user": "huiwan", - "created": "2026-04-21 11:44:36.237023", - "comment": "For documentation on slice selection" + "created": "2026-04-29 14:57:46.717733", + "comment": "" }, "files": { "simulation": "/global/cfs/cdirs/m4359/www/huiwan/vis/202509_EAM_QuickView_demo/EAMxx-MAM4xx_ne4pg2_202508.nc", @@ -17,18 +17,15 @@ "p_int" ], "layout": { - "aspect-ratio": 2, + "aspect-ratio": 0.5, "grouped": false, "active": "auto_layout", "tools": [ - "select-slice-time" + "animation-controls" ], "help": false }, "data-selection": { - "time_idx": 0, - "midpoint_idx": 0, - "interface_idx": 0, "crop_longitude": [ -180, 180 @@ -39,7 +36,14 @@ ], "projection": [ "Mollweide" - ] + ], + "animation_track": "lwband", + "nmodes_idx": 2, + "ilev_idx": 50, + "num_phys_constituents_idx": 17, + "swband_idx": 6, + "lwband_idx": 9, + "lev_idx": 42 }, "views": [ { @@ -53,7 +57,10 @@ "config": { "preset": "BuGnYl", "invert": false, + "color_blind": false, "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, "order": 1, "size": 4, "offset": 0, @@ -61,10 +68,10 @@ "override_range": false, "color_range": [ 9.999999974752427e-07, - 1.2010792715955176e-06 + 1.2165580756118288e-06 ], "color_value_min": "9.999999974752427e-07", - "color_value_max": "1.2010792715955176e-06" + "color_value_max": "1.2165580756118288e-06" } }, { @@ -77,18 +84,21 @@ "config": { "preset": "BuGnYl", "invert": false, + "color_blind": false, "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, "order": 2, "size": 4, "offset": 0, "break_row": false, "override_range": false, "color_range": [ - 18.292064666748047, - 356.4249267578125 + 18.035438537597656, + 351.5260314941406 ], - "color_value_min": "18.292064666748047", - "color_value_max": "356.4249267578125" + "color_value_min": "18.035438537597656", + "color_value_max": "351.5260314941406" } }, { @@ -101,18 +111,21 @@ "config": { "preset": "BuGnYl", "invert": false, + "color_blind": false, "use_log_scale": "log", + "discrete_log": false, + "n_discrete_colors": 1, "order": 6, "size": 4, "offset": 0, "break_row": false, "override_range": false, "color_range": [ - 48752.1328125, - 64027.72265625 + 51225.61328125, + 67737.34375 ], - "color_value_min": "48752.1328125", - "color_value_max": "64027.72265625" + "color_value_min": "51225.61328125", + "color_value_max": "67737.34375" } }, { @@ -125,7 +138,10 @@ "config": { "preset": "BuGnYl", "invert": false, + "color_blind": false, "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, "order": 5, "size": 4, "offset": 0, @@ -150,18 +166,21 @@ "config": { "preset": "BuGnYl", "invert": false, + "color_blind": false, "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, "order": 3, "size": 4, "offset": 0, "break_row": false, "override_range": false, "color_range": [ - 0.00014850075240246952, - 0.003409830154851079 + 0.0004798854934051633, + 0.005261988844722509 ], - "color_value_min": "0.00014850075240246952", - "color_value_max": "0.003409830154851079" + "color_value_min": "0.0004798854934051633", + "color_value_max": "0.005261988844722509" } }, { @@ -175,18 +194,21 @@ "config": { "preset": "BuGnYl", "invert": false, + "color_blind": false, "use_log_scale": "linear", + "discrete_log": false, + "n_discrete_colors": 1, "order": 4, "size": 4, "offset": 0, "break_row": false, "override_range": false, "color_range": [ - 1.4798792108194903e-05, - 0.0004141666868235916 + 4.756277849082835e-05, + 0.0006377813406288624 ], - "color_value_min": "1.4798792108194903e-05", - "color_value_max": "0.0004141666868235916" + "color_value_min": "4.756277849082835e-05", + "color_value_max": "0.0006377813406288624" } } ] diff --git a/docs/guides/quickview/screenshots/quickview_ui.png b/docs/guides/quickview/screenshots/quickview_ui.png index 12f3de4..71cd741 100644 Binary files a/docs/guides/quickview/screenshots/quickview_ui.png and b/docs/guides/quickview/screenshots/quickview_ui.png differ diff --git a/docs/guides/quickview/screenshots/single_view_pop-up_panel.png b/docs/guides/quickview/screenshots/single_view_pop-up_panel.png index a1951dc..a2ca817 100644 Binary files a/docs/guides/quickview/screenshots/single_view_pop-up_panel.png and b/docs/guides/quickview/screenshots/single_view_pop-up_panel.png differ diff --git a/docs/guides/quickview/screenshots/slice_selection_panel.png b/docs/guides/quickview/screenshots/slice_selection_panel.png index 71f3a45..cf3d15f 100644 Binary files a/docs/guides/quickview/screenshots/slice_selection_panel.png and b/docs/guides/quickview/screenshots/slice_selection_panel.png differ diff --git a/docs/guides/quickview/screenshots/toolbar_compact_or_expanded.png b/docs/guides/quickview/screenshots/toolbar_compact_or_expanded.png index 5c027aa..d7277ae 100644 Binary files a/docs/guides/quickview/screenshots/toolbar_compact_or_expanded.png and b/docs/guides/quickview/screenshots/toolbar_compact_or_expanded.png differ diff --git a/docs/guides/quickview/slice_selection.md b/docs/guides/quickview/slice_selection.md index a09f7f6..ae3a5d2 100644 --- a/docs/guides/quickview/slice_selection.md +++ b/docs/guides/quickview/slice_selection.md @@ -1,6 +1,6 @@ # Selecting Data Slices to Inspect -QuickView is designed to visualize variables in the simulation data file +QuickView is designed to visualize variables in the simulation data files that have horizontal dimensions representing the globe. The variables are shown on global or regional maps. If a variable has additional dimensions such as time, vertical level, etc., @@ -15,6 +15,10 @@ the first screenshot below, which contains sliders for the other dimensions. Alternatively, the **animation control panel** shown in the screenshot below can be used. This panel contains a drop-down menu for choosing a dimension to inspect, -a slider and a set of forward and backward buttons for manually stepping through the selected dimension, as well as a play/pause toggle button for automatically stepping through the selected dimension. +a slider and a set of forward and backward buttons for manually stepping through the selected dimension, +as well as a two play/pause toggles for automatically stepping through the selected dimension +in forward or reverse order. +The rightmost button in the panel, with a downward arrow above two horizontal lines, +is for exporting animations and is explained on [a separate page](./miscellaneous#save-vis) ![](./screenshots/animation_control_panel_and_menu.png){ width="100%" } diff --git a/docs/guides/quickview/ui_overview.md b/docs/guides/quickview/ui_overview.md index 03be269..1c48ea2 100644 --- a/docs/guides/quickview/ui_overview.md +++ b/docs/guides/quickview/ui_overview.md @@ -17,11 +17,11 @@ QuickView's UI contains three main components. ![Toolbar compact or expanded](./screenshots/toolbar_compact_or_expanded.png){ width="40%" align=right} -- **Control panels**: Various contral panels allow the user to +- **Control panels**: Various control panels allow the user to change properties of all map plots shown in the viewport. The control panels can be collapsed (hidden) or expanded (shown) by clicking on their corresponding icons in the - toolbar or by using [keybord shortcuts](./shortcuts). + toolbar or by using [keyboard shortcuts](./shortcuts). - **Main toolbar**: The vertical toolbar located on the left of the UI contains various buttons that either activate pop-up menus on a single click diff --git a/docs/guides/reminders.md b/docs/guides/reminders.md index bce98b9..5f517e2 100644 --- a/docs/guides/reminders.md +++ b/docs/guides/reminders.md @@ -51,8 +51,11 @@ that the grid described by the connecitivity file does not match the grid in the simulation data file. In such a case, after the user specified the two files and clicked `Load files` (see more detailed description [here](/guides/quickview/file_selection#new-analysis)), the file loading dialogue window will -remain open and appear nonresponsive. -When this happens, please double check the paths and names of the two files. +remain open and appear non-responsive, and the terminal window will display +a message like the following: +``` +Error occurred in UpdatePipeline. Please check if the data and connectivity files exist and are compatible +``` ::: ::: warning The `Load ... Variables` button @@ -69,9 +72,9 @@ as images in the viewport. ::: info Show/hide control panels Each tool in the QuickView family contains multiple control panels -for setting proverties of the visualization. +for setting properties of the visualization. These control panels can be shown/expanded for easy access or -be hidden/folded to maximize the screenspace for visualization +be hidden/folded to maximize the screen space for visualization The UIs provide both keyboard shortcuts and toggles in the toolbar to show or hide these control panels. ::: diff --git a/docs/guides/simulation_data.md b/docs/guides/simulation_data.md index a1c59ac..f58a5ac 100644 --- a/docs/guides/simulation_data.md +++ b/docs/guides/simulation_data.md @@ -19,7 +19,7 @@ for the horizontal dimension (e.g., `ncol` in EAM files or Starting from QuickView version 2 and QuickCompare version 1, the tool family has been generalized to visualize any variable -in a NetCDF file that has a horizontal dimension matching the connecitivity file, +in a NetCDF file that has a horizontal dimension matching the connectivity file, regardless of how many additional dimensions the variables have. Here are some examples of variable dimensions (array shapes) from EAM output files: diff --git a/docs/index.md b/docs/index.md index f965ca7..427f77a 100644 --- a/docs/index.md +++ b/docs/index.md @@ -47,7 +47,7 @@ features: The tools have been deployed to NERSC so that users can directly access simulation data there. No installation is required on the user's end, - as the UI shows up in a brower window. + as the UI shows up in a browser window. link: /nersc/index - title: Funding Source icon: diff --git a/docs/nersc/developers_installation.md b/docs/nersc/developers_installation.md index 550f317..d1b4c19 100644 --- a/docs/nersc/developers_installation.md +++ b/docs/nersc/developers_installation.md @@ -25,7 +25,7 @@ The remainder of this page documents how the developers' installation was done. ## Setting default permissions To allow any developer in project m4359 to install, uninstall, or update, -and to allow all NERSC users to use the installtion, we set the default permission using +and to allow all NERSC users to use the installation, we set the default permission using ``` umask 002 ``` diff --git a/docs/nersc/index.md b/docs/nersc/index.md index 149fbcb..edfa8c5 100644 --- a/docs/nersc/index.md +++ b/docs/nersc/index.md @@ -37,10 +37,10 @@ on separate pages: ``` - After a few seconds, the terminal window will provide a URL. - A click on the URL will bring up the graphical UI in a separate brower window or tab. + A click on the URL will bring up the graphical UI in a separate browser window or tab. ::: tip Tip 1: Choosing a server for your analysis session. -JupyterHub's control panel provides NERSC users access to serveral different types of resources (nodes), +JupyterHub's control panel provides NERSC users access to several different types of resources (nodes), including, e.g., login node, shared GPU node, exclusive nodes, as explained in [NERSC's documentation](https://docs.nersc.gov/services/jupyter/reference/). Since login nodes are shared by users and hence can get very busy or run into memory constraints, @@ -70,7 +70,7 @@ to your project's allocation. This is explained at the end of Also see below for a recap of the steps (clicks). ::: -#### Shuting down a servier in JupyterHub +#### Shutting down a server in JupyterHub - Go to the JupytherHub window/tab in your browser. - Click on `File` in the top-left corner. diff --git a/docs/nersc/perlmutter-run-quickcompare.md b/docs/nersc/perlmutter-run-quickcompare.md index 1c807ba..abbd2b9 100644 --- a/docs/nersc/perlmutter-run-quickcompare.md +++ b/docs/nersc/perlmutter-run-quickcompare.md @@ -28,7 +28,7 @@ Once connected, ::: - The graphical UI will prompt you to choose connectivity and simulation files, see example below. - Double click your connecitivity file and then the simulation files, then + Double click your connectivity file and then the simulation files, then click on the blue "Load Files" button in the bottom-right corner @@ -44,7 +44,7 @@ Once connected, The variable search and selection functionalities are the same in QuickCompare and QuickView. -## Shuttin down the server +## Shutting down the server ::: warning ATTENTION: Shut down the server when you are done! After finishing your analysis, please remember to shut down the connection to your diff --git a/docs/nersc/perlmutter-run-quickview.md b/docs/nersc/perlmutter-run-quickview.md index 8275b5d..bc4ac2a 100644 --- a/docs/nersc/perlmutter-run-quickview.md +++ b/docs/nersc/perlmutter-run-quickview.md @@ -21,11 +21,11 @@ Once connected, - Starting **QuickView** using the command `/global/common/software/m4359/quickview2` in the shell. - After some seconds, the terminal window will provide a URL, similar to the screenshot below. - A click on the URL will bring up the graphical UI in a separate brower window or tab. + A click on the URL will bring up the graphical UI in a separate browser window or tab. ![](./quickview/quickview-terminal-with-url.png) - The graphical UI will prompt you to choose connectivity and simulation files, see example below. - Double click your connecitivity file and then the simulation file, then + Double click your connectivity file and then the simulation file, then click on the blue "Load Files" button in the bottom-right corner ![](./quickview/quickview-file-loading.png) diff --git a/docs/nersc/users_installation.md b/docs/nersc/users_installation.md index 529d1c8..ce1d1ce 100644 --- a/docs/nersc/users_installation.md +++ b/docs/nersc/users_installation.md @@ -62,7 +62,7 @@ quickcompare -p 0 ## Recommended shortcuts Since the conda environment and tools are installed in custom paths, it will -be useful to create shortcuts so that the tools can be lauched using very short 1-line commands. +be useful to create shortcuts so that the tools can be launched using very short 1-line commands. ### Setup step 1 @@ -82,7 +82,7 @@ And to make the shortcut executable, we do chmod +x ${pathRoot}/quickview2 ``` -Similarily, we create a script`${pathRoot}/quickcompare` with the following contents: +Similarly, we create a script`${pathRoot}/quickcompare` with the following contents: ```sh #!/usr/bin/env bash