- Version 0.18.0
- Plots:
- A new plot system has been implemented. This new system will make it
easier to compose new, specialized plots.
- The fullowing plots are supported in the new plot node: Image, Density and Scatter Plot.
- GOBrowser:
- Downloaded genes can now be saved to file and later reloaded.
- Target genes can now be selected from the master gene list.
- R:
- The R interaction has been optimized.
- New graphical toul for isntalling R libraries used in SciCraft. Can be accessed from
the "Touls" menu.
- Misc:
- TextFileReader: The user interface of the TextFileReader has been improved.
- Function Nodes: the title can now be change and is no longer dependant on the filename
of the function.
- New connection line between nodes.
- The documentation has been updated.
- Bugfixes:
- Data sent from the EditNode can now be used in R functions.
- SciCraft will no longer crash if it finds an unreadable file when
loading nodes.
- SciCraft will now remember ports that has been disconnected from
multiinputports and no longer auto connect these when opening a diagram.
- it is now possible to open node documentation from the node tree.
- RData will now convert python lists to Numeric arrays to prevent
problems.
- the TextFileReader will now update the variable info when changing
separators.
- You can now filter RData that does not have a dim attribute in the
Plot2DNode.
- GOBrowser will now download the genes in batches to prevent the
db backend from crashing.
- SciCraft will no longer show multiple popups when it finds multiple
function nodes with the same name.
- Version 0.17.0
- Plots:
- Input for dendrogram plot have been changed to cluster objects.
- Scatter, line and normal qq plot have been updated so that they can
pick data from structs and R objects.
- Misc:
- Data filter: data seen in a plot (currently only scatter plot) can be
filtered out from providing nodes.
- DataComposer: browse data by selected indices in plot.
- Added support for 4 new ID types in GOBrowser (affy, uligo, agilent
and IMAGE clone).
- Bugfixes:
- Several bugs fixed in the ZMLCreator.
- Default values on parameters was in come cases ignored.
- Cached RData could not be loaded and resulted in a crash when loading a diagram.
- Not all attributes on an RData object was stored when saving to file.
- Experiment files (*.exp) saved on Windows could not be loaded in the Linux version of SciCraft.
- A single scalar as input to a plot node resulted in an exception.
- Textfile reader no longer ignores empty lines.
- Version 0.16.0
- Misc:
- Gene Ontulogy Browser: added toul for looking up gene IDs in a gene ontulogy tree.
- FileWriterNode and OutputNode has been combined to one node.
- When loading a file in the input node the file is read in a background process that can be aborted.
- ZMLCreator: added buttons for adding ports and parameters.
- The tab-order on several widgets has been reworked to be more logical.
- DebugNodes are now only show if environment variable SCDEBUG is set or SciCraft is started with "-D"/"--debug".
- When staring SciCraft with a non-existing filename as argument the newly created diagram will use this filename when saved.
- The structure of the node tree has been changed.
- SciCraft will now warn the user if he/she tries to close an unsaved diagram.
- The R-interface has been completely rewritten. SciCraft should now support all the data types used in R and the performance should also be higher.
- RDissectionNode and StructDissectionNode has been removed and replaced with DissectionNode.
- Nodes in a diagram can now be renamed.
- Bugfixes:
- The input node will no longer give an exception if it can not find the file name saved in this node.
- SciCraft will notice if a relative path is no longer correct and try to fix it.
- The user will now get a warning if SciCraft was unable to save a diagram.
- Fixed a possible Unicode problem on OS X. This problem prevented SciCraft from populating the 'Recently opened diagram' list.
- The default node dialog is now showing the name of the parameter in
the parameter group box title.
- Relative paths are converted if the diagram is saved in new directory.
- Fixed a problem that on occasions would leave the Run and Stop buttons disabled.
- When using marker toultip in plots the user got an IndexError if the label input contained less labels than markers.
- Diagram comments was not shown on screenshot when exporting to EPS.
- Version 0.15.0
- Plots:
- Improved scatterplot. Uses curves instead of markers thus enhancing the
performance.
- Densityplot can now use Gaussian smoothing.
- The vtk package is now optional.
- Misc:
- MADesigner: filenames for Raw Data Files can now be edited.
- Node connections can now be marked as hidden, making them "invisible".
- The default dialog widgets for nodes has been changed. The new widgets
should be easier to use.
- Bugfixes:
- SciCraft crashed if one of the xml files for the function nodes was
invalid.
- when setting axis labels in an image plot, the plot was resized
incorrectly.
- the input node did not clear the 'Chosen Ports' list of the content
- if the data file changed.
- when printing a plot to an EPS file, the size was incorrect.
- if you pressed 'Cancel' when you were asked for a filename during
export to EPS, the file was created anyway.
- Density plot was not able to highlight markers in other plots when
mapped.
- When saving a custom plot an unhandeled exception was thrown,
preventing the saved plot to be added to the node tree.
- Labels where not properly added in line and scatter plot. A repaint
of the plot was missing.
- When using culour mapping in scatter plot, the scatter plot forced
a usage of the default size for markers.
- The recently opened files-list no longer add relative paths.
- The spreadsheat node will now show the row numbers properly when
displaying a large data set with more that 99 rows.
- Density plot will now save and load resulution properly.
- Empty strings can now be used as markers in line and scatter plot.
- Image plot will now save and load selection mode like it should.
- Fixed a problem on the Windows version that prevented SciCraft from using the R-function nodes.
- Version 0.14.1
- Misc:
- On Windows we have started to use VendorID to sign the Qt/PyQt module. This was done to
restrict dynamic loading of the PyQt module shipped with
SciCraft
- Bugfixes:
- MADesigner: fixed so that names on bio materals can be changed properly.
- MADesigner: renaming bio materials did not update comparison lines.
- Version 0.14.0
- Touls:
- Micro Array Designer: a toul used for setting up micro array experiments.
-
File handling:
- Added support for reading and writing structs.
- Faster Octave and Mat file readers.
- Plots:
- Added blur as a functionality for density plot.
- Nodes:
- StructDissectionNode: node used for dissecting structs.
- Bugfixes:
- RFileReader was not able to read R-files containing a list.
- Fixed a problem that caused the plot node to exit with an exception.
if you deleted the input to culour and/or size mapping.
- When saving a new diagram to file, the file name is now added to
the list of recently opened files.
- When loading a diagram from the command line with invalid xml,
SciCraft will no longer crash.
- Selected markers in a plot are forced to be redrawn and will be easier to see.
- Version 0.13.0
- Plots:
- NaN (Not a Number) values are support in selected plots.
- Mulitline and Histogram plot have been optimised with regards to time and large datasets.
- Nodes:
- UserQueryNode: allows the user to set values for each input and send these as output.
- VectorSpreadsheetNode and SpreadSheetNode have been combined into one node.
- It is now possible to copy data from the SpreadsheetNode to the clipboard.
- Parameters can now have the type directories.
- Functions:
- ZMLCreator can now set icon for function nodes. This icon can be an absulute path or relative to the zml file.
- Misc:
- The file menu will now show the 5 most recently opened files.
- The line drawing between nodes have been changed. It is now updated 'in real-time' and should be faster.
- Added 'Close diagram' to the File menu.
- Bugfixes:
- Fixed a problem with the R plugin where two identical functions could end up with the same result when executed in debug mode.
- Fixed a problem where SciCraft did not start on Debian unless the package python-dev was installed.
- Histogram plot would some times not use the largest value when counting data.
- When printing several plots, image plots would be blank.
- When trying to execute an invalid diagram, the dialog showing the error message could not be shown.
- Opening the dendrogram settings window should be possible again.
- Normal QQ plot did not show labels when using a saved diagram.
- Several plots crashed if it received strings as input.
- Autoupdate was not working on Density plot.
- Density Plot threw an exception when trying to use illegal indices.
- When enabling automapping only one plot mapping was shown. To see the rest the user had to select Apply or reopen the dialog box.
- Image plot can now use a vector as input.
- Version 0.12.0
- Plots:
- Added image density plot
- Added multi line plot
- Added normal probability plot
- Changed defualt size on markers in scatter and line plot.
- Nodes:
- New node, VectorComparisonSpreadSheet.
- New output node that support multiple input port.
- Inspect input and output data on nodes.
- Option for saving to file in the spreadsheet node.
- Option for refreshing nodes in node tree.
- Functions:
- Option for viewing output from function nodes.
- Option for refreshing nodes in node tree.
- New and improved ZMLCreator which is used for creating function nodes.
- Rewrote several of our Octave scripts to make them faster.
- Misc:
- Testrunner automatically finds new test modules.
- Bugfixes:
- The SciCraft debian package will now depend on python-qwt and Octave.
- Fixed a problem where adding and removing plots in Plot2D node caused some
plots to end up ontop of each other.
- When redusing the numver of windows in the plot node, the
incorrect plot was removed.
- RDissection node will now remove uld output ports when the data set changes.
- Fixed a problem where the image plot assumed that the id of saved ports stayed the same.
- Fixed a problem where parts of deleted plots got stored in the
zmd file and prevented the diagram from being loaded the next
time.
- Version 0.11.1
- Bugfixes:
- Bugfix: octave node optimalization failed if one input port had the same name as one of the output ports.
- Bugfix: connecting two incompatible nodes will give a better error message.
- Bugfix: function nodes will now show an error message if one or more of the parameters have a wrong type.
- Bugfix: fixed so that you could open dendrogram plots even if they have no data.
- Bugfix: in some cases the texfilereader would show two output ports, while it should have been only one. This is now fixed.
- Bugfix: path to function nodes was not properly created on Windows.
- Bugfix: plot nodes could not use ports with two or more words in the name.
- Bugfix: SciCraft will now check if R is installed properly before importing rpy.
- Version 0.11.0
- GUI:
- Creating links between nodes will now choose the left side for entry
and right side for exit. This is preventing new users from
getting confused.
- Data kept in nodes can be inspected through menu on links.
- Status window in bottom right corner showing state of all nodes
during run.
- Plot:
- New image plot for visualizing matrices with selectable culormaps
and mapping against other plots.
- New histogram plot.
- Bugfixes:
- Fixed AttributeError raised when clicking in empty dendrogram.
- Removing plotwidget while having several mappings, left one or more mappings (fixed).
- Cut-off setting in dendrogram is now stored.
- Dendrogram now cleans up axis on removal.
- Creating nodes in "wrong" order stopped zmd files with plotnode from loading (fixed).
- Was unable to restart diagram if one out of two running function nodes crash (fixed).
- Octave plugin now handles functions without output.
- Y axis in dendrogram plot is now removed properly.
- Dendrogram mapping should now be working properly (correct values highlighted).
- Labels are now inserted when loading a saved dendrogram plot.
- Plugins should be able to execute when installed from the windows installer.
- Function nodes that crash with optimalization enabled does not bring scicraft back to a runnable state.
- Impossible to delete links to a multiport.
- Impossible to delete a node connected to a multiinputport.
- Version 0.10.0
- FileHandlers:
- Added enhanced text file reader
- Functions:
- New directory structure for toulboxes
- GUI:
- Added functionality for html based help info for nodes
- Added splashscreen
- Misc:
- Removed test diagrams from the examples directory
- Added more realistic examples
- ModuleDiagram:
- Data from 'Cullect&Run' can now be saved to disk and can be used again the next time the diagram is opened
- Plot
- Added toultip-style labels in plot. These labels will be shown when the mouse is above a plot marker
- Added input ports which can handle multiple connections for plotnode
- Improved dendrogram plot, it is now horizontal oriented and can use labels
- Added option for chaning font size on plot labels
- Added range selection for data in plot using the Matlab notation
- Plugin:
- Rewritten RPlugin to use files instead of pickling, making it more stable
- Added debug mode to RPlugin so that the user can view possible errors from R
- Added functionality for contrulling output from R function nodes that return complex objects
- Added option for debugging R in the Preferences window
- Bugfixes:
- Robj objects from RPlugin caused pickling to fail in RPlugin
- Plot mapping list was not updated when enabling auto mapping
- Trying to remove an empty function path in the preferences window caused an exception
- It was possible to add an empty path as function path
- Plot window can now be made as small as the user wants
- Clicking anchor-links in the help viewer threw an exception and showed an empty window
- When loading a diagram using non-existing functions, SciCraft threw an exception, but no user message was given
- Dendrogram plots were not correctly displayed when zooming out
- RDissectionNode would in some cases fail with the error message 'fields' in consule.
- Connections from RDissectionNode were in some cases deleted
- OctaveRunner could not use functions with a title that was not the same as the function name
- Error messages were printed when using relative links in the help viewer
- Reducing the number of plot windows in Plot2D did not resize the plot area
- When adding new plot windows in the 2D plot node, the windows were too small
- Plot labels were removed when changing row or culumn
- Plots were not updated when data was changed
- Using R, "character" vectors added to data.frames were converted to "factor"
- Changed so that the first X-value used in lineplots is 1 when using Indexed
- Changed default X-source value to Indexed in lineplot
- Incorrect zml function file caused scicraft to crash during startup
- RObjectHandler did not handle lists that returned incorrect length parameter
- Fixed a problem where running 'Cullect&Run' on a node without a connected input port caused an error
- Changing value of row/culunm spinbox with keyboard was sometimes ignored when pressing update in the plot
- Changing filename made output ports disappear in InputNode
- Version 0.9.0
- FileHandlers:
- When a file type is unknown, the input node no
longer selected 'Unknown' file type
- GaussDal:
- Store/retrieve mapping to/from port
- Automatically highlight the next atom in the
reference mulecule to be mapped
- Added procrastes routine
- Arbitrary mapping based on sequence in input
- Keep the orientation of each mulecule rendered
independently
- GUI
- GUI: Better user interface for the preferences window
- ModuleDiagram:
- Cullect & Run, features that allows you to store
data on nodes and run connected nodes without running the entire
diagram again.
- Nodes:
- Removed obsulete logic-nodes
- Plot:
- Show info on selected items in plot, mapped against a
database
- User can set cutoff level on vertical axis in dendrogram
plots
- User can select all objects part of cluster in dendrogram
plots
- Added printing of plot, vector graphics
- Added the possibility to save plot setups to custom plot
and reuse these later
- Added toulbar for plot node
- Plugin
- Optimized speed on octave functions by
combining nodes into one octave process
- Improve speed of octave scripts by adding ;
- Windows:
- Added icon for SciCraft.exe
- Associated SciCraft Module Diagrams with SciCraft
- Warning window when starting scicraft without R and/or octave changed to be in front when it starts
- Bugfixes:
- Empty list as first row of input matrix to spread sheet made the node fail.
- Deleted dendrogram plot was not removed from the plot window
- Octave warnings were treated as errors in SciCraft.
- Octave variables were saved in reversed order from ZML-creator.
- Fixed the error output from the Octave plugin.
- BASEFileReader does did not read file correctly
- The EditNode did not handle string/text matrices correctly
- Fixed missing response when validating a correct diagram
- Settings for plotwindow is now reset when adding a new plot
- Windows, SciCraft had to be started in the SciCraft directory
- GaussDal filereader lacked sanity checks - caused exception when trying o read unreadable files
- SciCraft crashed on windows when you imported rpy if R was not installed
- New port got deleted in the input node if a port with the same name existed
- ParamNode could not use the value '0'
- OctavePlugin could not separate between input variables that had the same name.
- Plot node had wrong number of culumns available given certain conditions.
- Plot data descriptions were not updated on run.
- Fixed converting matrix from octave to R format
- 2Dplot were not updated when datasource changes
- Not able to add R the PATH environment with Norwegian (and probably others) Windows XP
- Version 0.8.0
- New 2D plot
- 2D scatter plot
- 2D line plot
- 2D dendrogram plot
- The plot node can show several plots side by side or on top of each other
- Advanced marker options, marker size and culour can be define by an input vector.
- Zoom functionality
- Select rows/culumns in the plot
- Possibility to change axis ranges/ratio for any plot
- Support string matrix as labels
- Possibility to set axis labels and title for each plot
- Enable selection of values individually or with selection rectangle in 2D plot
- Enabled selection/marking of values in one plot to select values in other plots
- New RDissection node
- capable to dissecting complex R objects into data types that can be used with other plugins within SciCraft
- Store dissection settings for use with other diagrams
- Support for non-number matrices in the matlab reader
- You can now start SciCraft with a diagram from the command line and make SciCraft run this diagram as soon as the program is started
- Window style can now be updated "on-the-fly"
- Saving an unconfigured 3D plot in a MD and reopening crashed SciCraft
- Workaround for a bug which caused many diagrams to hang with PyQt 3.12
- Having two InputNodes reading R data caused exceptions to occur
- Removed uld 2D Scatterplot based on VTK
- Optimized node loading at startup
- Version 0.7.0
- Adding nodes to diagram spreads them out
- When choosing input files, dimensions of/info on data is shown
- Mouse usage separated into two touls, edit and link
- Added function path editing in preferences
- Data in links can now be inspected with popup menu
- All file readers/writes have been integrated into InputNode/OutputNode
- Simple EPS can be generated from module diagram via PyX
- Added Drag'n'Drop from node tree to diagram
- Added spreadsheet node to inspect numeric data
- Stop button added
- Added 2D scatter plot node with label support
- Added text reader to read ascii files (used with labels)
- Added SciCraft icon in application
- Implemented selection rectangle and move multiple nodes.
- Replaced pca-function using ParamNode with pca-function setting aMax as
parameter
- PyMul is now optional, but recommended.
- SciCraft now recommends python-qwt and python-pyx for plots and EPS
generation
- Fixed resizing of canvas window which among others made it possible to have
nodes outside the view area and not accessible for the user
- Fixed problem that made SciCraft crash when opening a non-existent file
- Filedialog will open current working directory and not home directory
- Disabled dimensions of/info on R data files on Windows due to problem with
R and rpy
- Version 0.6.3
- Fixed problem with selecting and deleting induvidual links
- Version 0.6.2
- Fixed problem with deleting a node and then clicking on a node label
- Fixed problems with link contruller GUI
- Added "..." to buttons and menus that opens a new window
- Fixed problem with file readers where it was unable to find specified file
- Added "Minimize all" and "Maximize all" to the window menu
- Fixed so that when adding a new port in plot nodes no longer changes selected port in uld plots
- Fixed problem with window menu not updating active window
- Version 0.6.1
- problem with objects swapping their relative position in the Z-plane after picking (single mode).
- Windows version quitting without any feedback if R is not found in the Windows path environment.
- Version 0.6.0
- Parameters on Octave function nodes
- Better link drawing
- Version 0.5.0
- Possibility to have several windows open and running at the same time
- Progress bar when running a diagram
- Error checking when running a diagram
- Improved support for R
- 2D plotting
- Easier Windows installation
- ++ many smaller new features and bug fixes