pyworkflow.utils.properties module

This module defines the text used in the application.

class pyworkflow.utils.properties.Color[source]

Bases: object

DARK_GREY_COLOR = '#6E6E6E'
LIGHT_BLUE_COLOR = '#EAEBFF'
LIGHT_GREY_COLOR = '#EAEBEC'
LIGHT_GREY_COLOR_2 = '#F2F2F2'
LIGHT_RED_COLOR = '#F3CBCB'
RED_COLOR = 'Firebrick'
STATUS_ABORTED = ('#F5CCCB',)
STATUS_FAILED = ('#F5CCCB',)
STATUS_FINISHED = ('#D2F5CB',)
STATUS_INTERACTIVE = ('#F3F5CB',)
STATUS_LAUNCHED = ('#D9F1FA',)
STATUS_RUNNING = ('#FCCE62',)
STATUS_SAVED = ('#D9F1FA',)
class pyworkflow.utils.properties.Icon[source]

Bases: object

ACTION_BROWSE = 'fa-folder-open.gif'
ACTION_CLOSE = 'fa-times.gif'
ACTION_CONTINUE = 'fa-play-circle-o.gif'
ACTION_COPY = 'fa-files-o.gif'
ACTION_DB = 'fa-database.gif'
ACTION_DELETE = 'fa-trash-o.gif'
ACTION_EDIT = 'fa-pencil.gif'
ACTION_EXECUTE = 'fa-cogs.gif'
ACTION_EXPORT = 'fa-external-link.gif'
ACTION_EXPORT_UPLOAD = 'fa-upload.gif'
ACTION_FIND_NEXT = 'fa-next.gif'
ACTION_FIND_PREVIOUS = 'fa-previous.gif'
ACTION_HELP = 'fa-question-circle.gif'
ACTION_IN = 'fa-sign-in.gif'
ACTION_LIST = 'fa-bars.gif'
ACTION_NEW = 'fa-plus-circle.gif'
ACTION_OUT = 'fa-sign-out.gif'
ACTION_REFERENCES = 'fa-external-link.gif'
ACTION_REFRESH = 'fa-refresh.gif'
ACTION_RENAME = 'rename.gif'
ACTION_RESULTS = 'fa-eye.gif'
ACTION_SAVE = 'fa-save.gif'
ACTION_SELECT_TO = 'fa-arrow-up.gif'
ACTION_STEPS = 'fa-list-ul.gif'
ACTION_STOP = 'fa-stop.gif'
ACTION_STOP_WORKFLOW = 'fa-stop-workflow.gif'
ACTION_TREE = None
ACTION_UNDO = 'fa-undo.gif'
ACTION_VISUALIZE = 'fa-eye.gif'
ACTION_WIZ = 'fa-magic.gif'
ARROW_LEFT = 'fa-arrow-left.gif'
ARROW_UP = 'fa-arrow-up.gif'
BRUSH = 'fa-paint-brush.gif'
BUTTON_CANCEL = 'fa-ban.gif'
BUTTON_CLOSE = 'fa-times.gif'
BUTTON_PC = 'fa-laptop.gif'
BUTTON_SAVE = 'fa-save.gif'
BUTTON_SELECT = 'fa-check.gif'
CHECKED = 'fa-checked.gif'
DELETE_OPERATION = 'fa-delete-operation.gif'
FAILURE = 'fa-failure.gif'
HOME = 'fa-home.gif'
INSTALL = 'fa-install.gif'
INSTALLED = 'fa-installed.gif'
LIGHTBULB = 'fa-lightbulb-o.gif'
PLUS_CIRCLE = 'fa-plus-circle.gif'
PROCESSING = 'fa-processing.gif'
ROCKET = 'fa-rocket.gif'
ROOT = 'root.gif'
RUNS_LIST = 'fa-bars.gif'
RUNS_TREE = 'fa-sitemap.gif'
SCIPION_ICON = 'scipion_icon.gif'
SCIPION_ICON_PROJ = 'scipion_icon.gif'
SCIPION_ICON_PROJS = 'scipion_icon.gif'
SCIPION_ICON_PROT = 'scipion_icon.gif'
TAGS = 'fa-tags.gif'
TO_INSTALL = 'fa-to_install.gif'
TO_UPDATE = 'fa-update.gif'
UNCHECKED = 'fa-unchecked.gif'
UNINSTALL = 'fa-uninstall.gif'
class pyworkflow.utils.properties.KEYSYM[source]

Bases: object

Keysym values for evaluating key pressed within events as reported at http://infohost.nmt.edu/tcc/help/pubs/tkinter/web/key-names.html

DELETE = 'Delete'
RETURN = 'Return'
class pyworkflow.utils.properties.Message[source]

Bases: object

CANCEL_SELECTED_OPERATION = 'Cancel a selected operation'
ERROR_DIMENSIONS = 'Incorrect table width or height: '
ERROR_IMPORT_VOL = 'importVolumes:There is not filePaths matching pattern'
ERROR_NO_EST_CTF = '_estimateCTF should be implemented'
ERROR_PATTERN_EMPTY = 'The *pattern* cannot be empty.'
ERROR_PATTERN_FILES = 'There are no files matching the *pattern*'
ERROR_WEBGL = 'Your web browser does not support or is not configured for WebGL. See [[http://get.webgl.org/][WebGL Support]] for more information.'
EXECUTE_PLUGINS_MANAGER_OPERATION = 'Execute all selected operations'
HELP_MPI_THREADS = '\nDefine the number of processors to be used in the execution.\n*MPI*: This is a number of independent processes\n that communicate through message passing\n over the network (or the same computer).\n*Threads*: This refers to different execution threads \n in the same process that can share memory. They run in\n the same computer. \n '
HELP_RUNMODE = " \nNormally, each protocol is composed by several atomic steps.\nEach step could be computationally intensive, that's why\nthe *Continue* execution mode will try to continue from the\nlast completed step. On the other hand, the *Restart* mode\nwill clean the whole run directory and start from scratch. \n "
HELP_USEQUEUE = '\n Click *Yes* if you want to submit a single job per protocol to a Queue system.\n The queue commands for launch and stop jobs should be configured\n for the current host in the _%s_ file.\n '
HELP_USEQUEUEPERJOB = '\n Click *Yes* if you want to submit the multiple jobs per protocol to a Queue system.\n The queue commands for launch and stop jobs should be configured\n for the current host in the _hosts.conf_ file.\n '
HELP_WAIT_FOR = '\n Specify a comma separated list of protocol IDs if you want\nthat this protocol starts after the input protocols in the list\nare finished. This function will allow you to "schedule" many\nruns that will be executed after each other.\n '
LABEL_ALIG_PART = 'Write aligned particles?'
LABEL_AMPLITUDE = 'Amplitude Contrast'
LABEL_ANALYZE = 'Analyze Results'
LABEL_APPLY_TRANSFORM = 'Apply Transform Matrix'
LABEL_BIB_BTN = 'Export references'
LABEL_BLOCK_SELECTION = 'Select Block'
LABEL_BROWSE = 'Browse'
LABEL_BROWSE_ACTION = 'Browse '
LABEL_BUTTON_CANCEL = 'Cancel'
LABEL_BUTTON_CLOSE = 'Close'
LABEL_BUTTON_EXEC = 'Execute'
LABEL_BUTTON_HELP = 'Help'
LABEL_BUTTON_OK = 'Ok'
LABEL_BUTTON_RETURN = 'Save'
LABEL_BUTTON_SAVE = 'Save'
LABEL_BUTTON_VIS = 'Visualize'
LABEL_BUTTON_WIZ = 'Wizard'
LABEL_CHECKSTACK = 'Check stack files?'
LABEL_CITE = 'Cite'
LABEL_COLS = 'Cols'
LABEL_COMMENT = 'Comments'
LABEL_CONTINUE = 'Continue'
LABEL_CONTINUE_ACTION = 'Approve continue'
LABEL_CONTINUE_WORKFLOW = 'Continue workflow'
LABEL_COPY = 'Copy'
LABEL_COPYFILES = 'Copy files?'
LABEL_COPY_ACTION = 'Copy '
LABEL_CREATED = 'Created: '
LABEL_CREATE_PROJECT = 'Create Project'
LABEL_CTF_ESTI = 'CTF Estimation'
LABEL_DATA = 'Data'
LABEL_DB = 'Db'
LABEL_DEFAULT = 'Default'
LABEL_DELETE = 'Delete'
LABEL_DELETE_ACTION = 'Delete '
LABEL_DELETE_FORM = "\nYou are going to *DELETE* the run(s): \n - %s\n*ALL DATA* related will be permanently removed.\n\nDo you really want to continue?'\n"
LABEL_DELETE_PROJECT = '[Delete]'
LABEL_DISABLE = 'Disable'
LABEL_DISPLAY_TABLE_CONFIG = 'Display Table Configuration'
LABEL_EDIT = 'Edit'
LABEL_EDIT_ACTION = 'Edit '
LABEL_ENABLE = 'Enable'
LABEL_EXECUTION = 'Run mode'
LABEL_EXPERT = 'Expert Level'
LABEL_EXPERT_ADVANCE = 'Advanced'
LABEL_EXPERT_EXPERT = 'Expert'
LABEL_EXPERT_NORMAL = 'Normal'
LABEL_EXPORT = 'Export'
LABEL_EXPORT_UPLOAD = 'Export & upload'
LABEL_FOUND_ERROR = 'Errors found'
LABEL_HELP = 'Help'
LABEL_HOST = 'Host'
LABEL_IMPORT_PROJECT = 'Import project'
LABEL_INPUT = 'Input'
LABEL_INPUT_MIC = 'Input Micrographs'
LABEL_INPUT_MOVS = 'Input Movies'
LABEL_INPUT_PART = 'Input Particles'
LABEL_INPUT_VOLS = 'Input Volumes'
LABEL_INSPECTOR = 'Objects inspector will inspect the whole project. Thus, it can take a while depending on the size of the project.\nDo you want to continue?'
LABEL_LABEL = 'Label'
LABEL_LABEL_SELECTION = 'Select Label'
LABEL_LAUNCHED = 'The protocol was launched successfully.'
LABEL_LIST = 'List'
LABEL_LOGS = 'Output Logs'
LABEL_LOGS_ERROR = 'Error Log'
LABEL_LOGS_OUTPUT = 'Output Log'
LABEL_LOGS_SCIPION = 'Scipion Log'
LABEL_MAGNI_RATE = 'Magnification rate'
LABEL_METHODS = 'Methods'
LABEL_MIRRORY = 'Invert Y Axis'
LABEL_MODIFIED = 'Modified: '
LABEL_MPI = 'MPI'
LABEL_NEW = 'New'
LABEL_NEW_ACTION = 'New '
LABEL_OBJCREATED = 'Created'
LABEL_OBJINFO = 'Info'
LABEL_OBJLABEL = 'Label'
LABEL_OBJSUMMARY = 'Object Summary'
LABEL_ONLY_SHIFTS = 'Only Shifts'
LABEL_OPT_COMMENT = 'Describe your run here...'
LABEL_OUTPUT = 'Output'
LABEL_PARALLEL = 'Parallel'
LABEL_PARAM_NO = 'No'
LABEL_PARAM_YES = 'Yes'
LABEL_PATTERN = 'Pattern'
LABEL_PATTERNT = 'Pattern tilted'
LABEL_PATTERNU = 'Pattern untilted'
LABEL_PICK_GAUSS = 'Do you wish to perform an automatic gaussian picking for the remaining micrographs?'
LABEL_PROJECT = 'Project '
LABEL_PROJECTS = 'Projects'
LABEL_PROTTREE_NONE = 'None'
LABEL_QUEUE = 'Use queue?'
LABEL_QUEUE_FOR_JOBS = 'Use queue for Jobs?'
LABEL_QUEUE_NO = 'No'
LABEL_QUEUE_YES = 'Yes'
LABEL_REFRESH = 'Refresh'
LABEL_RENAME = 'Rename '
LABEL_RENAME_PROJECT = '[Rename]'
LABEL_RENDER = 'Render'
LABEL_RESET_WORKFLOW = 'Reset from here'
LABEL_RESLICE = 'Reslice'
LABEL_RESTART_FORM = "\nYou are going to *RESTART* the run: \n %s\n\nDo you really want to restart?'\n"
LABEL_RESTART_PROTOCOL = '\n Do you want to *RESTART* ONLY the run: \n %s \n *ALL DATA* related with the rest of protocols that depends on this, \n will be permanently removed. \n '
LABEL_RESTART_WORKFLOW = 'Restart workflow'
LABEL_ROWS = 'Rows'
LABEL_RUNMODE = 'Mode'
LABEL_RUNNAME = 'Run name'
LABEL_RUN_MODE_RESTART = 'restart'
LABEL_RUN_MODE_RESUME = 'resume'
LABEL_SAMP_MODE = 'Sampling rate mode'
LABEL_SAMP_MODE_1 = 'From image'
LABEL_SAMP_MODE_2 = 'From scanner'
LABEL_SAMP_RATE = 'Pixel size ("sampling rate") (Å/px)'
LABEL_SAVED_FORM = 'The protocol was saved successfully.'
LABEL_SAVE_OUTPUT = 'Do you wish to save protocol output?'
LABEL_SCANNED = 'Scanned pixel size (microns/px)'
LABEL_SELECT_ALL = 'Select all'
LABEL_SELECT_FROM = 'Select from here'
LABEL_SELECT_TO = 'Select to here'
LABEL_SMALLTREE = 'Small Tree'
LABEL_SPH_ABERRATION = 'Spherical aberration (mm)'
LABEL_STEPS = 'Steps'
LABEL_STOP = 'Stop'
LABEL_STOP_ACTION = 'Stop execution'
LABEL_STOP_FORM = 'Do you really want to *STOP* this run?'
LABEL_STOP_WORKFLOW = 'Stop from here'
LABEL_SUMMARY = 'Summary'
LABEL_THREADS = 'Threads'
LABEL_THRESHOLD = 'Threshold:'
LABEL_TREE = 'Tree'
LABEL_VISIBLE = 'Visible'
LABEL_VOLTAGE = 'Microscope voltage (kV)'
LABEL_VOLUME_SELECTION = 'Select Volume'
LABEL_WAIT_FOR = 'Wait for'
LABEL_WORKFLOW = 'Workflow View: '
LABEL_WRAP = 'Wrap'
MESSAGE_DELETE_PROJECT = 'This will *delete* the project and all its *data*. Are you sure?'
NO_INFO_LOGS = 'No logs information.'
NO_INFO_METHODS = 'No methods information.'
NO_INFO_SUMMARY = 'No summary information.'
NO_SAVE_SETTINGS = 'Error trying to save settings.'
NO_VIEWER_FOUND = 'There is not viewer for protocol:'
RESLICE_X_NEGATIVE = 'X Negative (Left)'
RESLICE_X_POSITIVE = 'X Positive (Right)'
RESLICE_Y_NEGATIVE = 'Y Negative (Top)'
RESLICE_Y_POSITIVE = 'Y Positive (Bottom)'
RESLICE_Z_NEGATIVE = 'Z Negative (Front)'
SHOWJ_TITLE = 'Showj'
TEXT_ALIG_PART = 'If set to *Yes*, the alignment will be applied to \ninput particles and a new aligned set will be created.'
TEXT_AMPLITUDE = 'Produced by the loss of amplitude (i.e. electrons) from the beam.\n\nFor a weak phase and weak amplitude object, the amplitude contrast ratio Qo\nis automatically computed. It should be a positive number, typically between\n0.05 and 0.3.'
TEXT_HELP = 'The file selected will be uploaded to the project folder. If the file was uploaded before, It will be replaced.'
TEXT_MAGNI_RATE = 'Electron optical magnification (M). It can be used to compute the Image Pixel\nSize ("Sampling Rate") (Ts) using the Scanner Pixel Size (Tm), Ts = Tm / M.\n\nIt is used by a few programs like Ctffind or Frealign.'
TEXT_NO_CTF_READY = 'CTF of *Input Micrographs* not ready yet.'
TEXT_NO_INPUT_MIC = 'No *Input Micrographs* selected.'
TEXT_NO_OUTPUT_CO = 'Output coordinates not ready yet.'
TEXT_NO_OUTPUT_FILES = 'No output file produced'
TEXT_PATTERN = 'Pattern (that can include wildcards) of the files to import.\nFor example:\n *data/particles/***.spi*\n *~/Micrographs/mic/***.mrc*'
TEXT_SAMP_MODE = 'You can specify the sampling rate (pixel size) directly from the image\n(A/pixel, Ts) or by specifying the magnification rate (M) and the scanner\npixel size (microns/pixel, Tm).\n\nThey are related by Ts = Tm / M'
TEXT_SAMP_RATE = 'Pixel size'
TEXT_SPH_ABERRATION = 'Optical effect due to the increased refraction of light rays when they\nstrike the lens near its edge, in comparison with those that strike near\nthe center.'
TEXT_VOLTAGE = 'Microscope voltage'
TITLE_BROWSE_DATA = 'Protocol data'
TITLE_COMMENT = 'Comment'
TITLE_CREATE_PROJECT = 'Enter the project name'
TITLE_CREATE_PROJECT_NAME = 'Project Name: '
TITLE_DELETE_FORM = 'Confirm DELETE'
TITLE_DELETE_PROJECT = 'Confirm project deletion'
TITLE_EDIT_OBJECT = 'Edit Object properties'
TITLE_EXEC = 'Execution'
TITLE_INSPECTOR = 'Objects inspector'
TITLE_LABEL = 'Label'
TITLE_LAUNCHED = 'Success'
TITLE_LAUNCHED_WORKFLOW_FAILED = 'The workflow can not be relaunch from this protocol.\n'
TITLE_LAUNCHED_WORKFLOW_FAILED_FORM = 'Error while launching the workflow'
TITLE_NAME_RUN = ' Protocol Run: '
TITLE_PICK_GAUSS = 'Automatic gaussian picking'
TITLE_RENAME_PROJECT = 'Confirm project renaming'
TITLE_RESETED_WORKFLOW_FAILED = 'Error while resetting the workflow'
TITLE_RESET_WORKFLOW = 'Do you really want to *RESET* this Workflow?'
TITLE_RESET_WORKFLOW_FORM = 'Confirm RESET'
TITLE_RESTART_FORM = 'Confirm RESTART'
TITLE_RESTART_WORKFLOW = 'Do you really want to *RESTART* this Workflow? All previous results will be deleted'
TITLE_RESTART_WORKFLOW_FORM = 'Confirm RESTART'
TITLE_RUN = 'Run'
TITLE_SAVED_FORM = 'Success'
TITLE_SAVE_OUTPUT = 'Save protocol output'
TITLE_STOPPED_WORKFLOW_FAILED = 'Error while stopping the workflow'
TITLE_STOP_FORM = 'Confirm STOP'
TITLE_STOP_WORKFLOW = 'Do you really want to *STOP* this Workflow?'
TITLE_STOP_WORKFLOW_FORM = 'Confirm STOP'
TOOLTIP_EXTERNAL = 'Open the viewer in an external window. '
TOOLTIP_REFRESH = 'Reload the content of the files in the viewer. '
TOOLTIP_SEARCH_NEXT = 'Move to the next highlighted item. Also, press <Down> or <F3>'
TOOLTIP_SEARCH_PREVIOUS = 'Move to the previous highlighted item. Also, press <Up> or <Shift-F3>'
VAR_COMMENT = 'comment'
VAR_EXEC_HOST = 'hostName'
VAR_EXPERT = 'expertLevel'
VAR_MPI = 'numberOfMpi'
VAR_QUEUE = '_useQueue'
VAR_RUN_MODE = 'runMode'
VAR_RUN_NAME = 'runName'
VAR_THREADS = 'numberOfThreads'
VIEW_DATA = 'Data'
VIEW_PROJECTS = 'Projects'
VIEW_PROTOCOLS = 'Protocols'
VIEW_UPLOAD = 'Upload'
class pyworkflow.utils.properties.PluginStates[source]

Bases: object

AVAILABLE_RELEASE = 'available_release'
BINARY = 'binary'
CHECKED = 'checked'
ERRORS = 'errors'
FAILURE = 'failure'
INSTALL = 'install'
INSTALLED = 'installed'
PLUGIN = 'plugin'
PRECESSING = 'processing'
SUCCESS = 'success'
TO_INSTALL = 'to_install'
TO_UPDATE = 'to_update'
UNCHECKED = 'unchecked'
UNINSTALL = 'uninstall'
class pyworkflow.utils.properties.colorText[source]

Bases: object

printing in colors, bold, etc, example: print colorText.BOLD + ‘Hello World !’ + color.END

BLUE = '\x1b[94m'
BOLD = '\x1b[1m'
CYAN = '\x1b[96m'
DARKCYAN = '\x1b[36m'
END = '\x1b[0m'
GREEN = '\x1b[92m'
PURPLE = '\x1b[95m'
RED = '\x1b[91m'
UNDERLINE = '\x1b[4m'
YELLOW = '\x1b[93m'