# -*- coding: utf-8 -*-
# **************************************************************************
# *
# * Authors: Jose Gutierrez (jose.gutierrez@cnb.csic.es)
# * Adrian Quintana (aquintana@cnb.csic.es)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
"""
This module defines the text used in the application.
"""
# NOTE: DO NOT REMOVE UNTIL plugin manager uses Config.SCIPION_MAIN_COLOR and is released
from pyworkflow.constants import Color
[docs]class Message:
# Example Usage:
# MyMessage = Message()
# print MyMessage.label
# Header List
VIEW_PROJECTS = 'Projects'
VIEW_PROTOCOLS = 'Protocols'
VIEW_DATA = 'Data'
VIEW_UPLOAD = 'Upload'
# Projects Template
LABEL_PROJECTS = 'Projects'
LABEL_CREATE_PROJECT = 'Create Project'
LABEL_IMPORT_PROJECT = 'Import project'
TITLE_CREATE_PROJECT = 'Enter the project name'
TITLE_CREATE_PROJECT_NAME = 'Project Name: '
TITLE_EDIT_OBJECT = 'Edit Object properties'
MESSAGE_DELETE_PROJECT = 'This will *delete* the project and all its *data*. Are you sure?'
LABEL_DELETE_PROJECT = '[Delete]'
TITLE_DELETE_PROJECT = 'Confirm project deletion'
LABEL_RENAME_PROJECT = '[Rename]'
TITLE_RENAME_PROJECT = 'Confirm project renaming'
LABEL_CREATED = 'Created: '
LABEL_MODIFIED = 'Modified: '
# Project Content Template
LABEL_PROJECT = 'Project '
# -- Protocol Treeview --
LABEL_WORKFLOW = 'Workflow View: '
LABEL_PROTTREE_NONE = 'None'
# -- Toolbar --
LABEL_NEW = 'New'
LABEL_NEW_ACTION = 'New '
LABEL_EDIT = 'Edit'
LABEL_RENAME = 'Rename '
LABEL_COPY = 'Copy'
LABEL_PASTE = 'Paste'
LABEL_DUPLICATE = 'Duplicate'
LABEL_DELETE = 'Delete'
LABEL_STEPS = 'Steps'
LABEL_BROWSE = 'Browse'
LABEL_DB = 'Db'
LABEL_STOP = 'Stop'
LABEL_ANALYZE = 'Analyze Results'
LABEL_TREE = 'Tree'
LABEL_SMALLTREE = 'Small Tree'
LABEL_REFRESH = 'Refresh'
LABEL_DEFAULT = 'Default'
LABEL_CONTINUE = 'Continue'
LABEL_EXPORT = 'Export'
LABEL_EXPORT_UPLOAD = 'Export & upload'
LABEL_RESTART_WORKFLOW = 'Restart workflow'
LABEL_CONTINUE_WORKFLOW = 'Continue workflow'
LABEL_STOP_WORKFLOW = 'Stop from here'
LABEL_RESET_WORKFLOW = 'Reset from here'
# -- Tabs --
LABEL_DATA = 'Data'
LABEL_SUMMARY = 'Summary'
LABEL_INPUT = 'Input'
LABEL_OUTPUT = 'Output'
LABEL_COMMENT = 'Comments'
LABEL_OBJSUMMARY = 'Object Summary'
LABEL_OBJINFO = 'Info'
LABEL_OBJCREATED = 'Created'
LABEL_OBJLABEL = 'Label'
LABEL_METHODS = 'Methods'
LABEL_BIB_BTN = 'Export references'
LABEL_LOGS = 'Output Logs'
LABEL_LOGS_OUTPUT = 'Output Log'
LABEL_LOGS_ERROR = 'Error Log'
LABEL_LOGS_SCIPION = 'Scipion Log'
NO_INFO_SUMMARY = 'No summary information.'
NO_INFO_METHODS = 'No methods information.'
NO_INFO_LOGS = 'No logs information.'
NO_SAVE_SETTINGS = 'Error trying to save settings.'
# ------- Protocol Form messages ----------
LABEL_CITE = 'Cite'
LABEL_HELP = 'Help'
TEXT_HELP = 'The file selected will be uploaded to the project folder. If the file was uploaded before, it will be replaced.'
LABEL_RUNNAME = 'Run name'
LABEL_EXECUTION = 'Run mode'
LABEL_RUNMODE = 'Mode'
LABEL_PARALLEL = 'Parallel'
LABEL_HOST = 'Host'
LABEL_THREADS = 'Threads'
LABEL_MPI = 'MPI'
LABEL_QUEUE = 'Use a queue engine?'
LABEL_QUEUE_FOR_JOBS = 'Use queue for Jobs?'
LABEL_WAIT_FOR = 'Wait for'
LABEL_EXPERT = 'Expert Level'
LABEL_EXPERT_NORMAL = 'Normal'
LABEL_EXPERT_ADVANCE = 'Advanced'
LABEL_EXPERT_EXPERT = 'Expert'
HELP_RUNMODE = """
Normally, each protocol is composed of several atomic steps.
Each step could be computationally intensive, that's why
the *Continue* execution mode will try to continue from the
last completed step. On the other hand, the *Restart* mode
will clean the whole run directory and start from scratch.
"""
HELP_MPI_THREADS = """
Define the number of processors to be used in the execution.
*MPI*: This is a number of independent processes
that communicate through message passing
over the network (or the same computer).
*Threads*: This refers to different execution threads
in the same process that can share memory. They run in
the same computer.
"""
HELP_USEQUEUE = """
Click Yes if you want to send this execution to a queue engine like Slurm, Torque, ...
The queue commands to launch and stop jobs should be configured at
_%s_ file.
See %s for more information.
"""
HELP_USEQUEUEPERJOB = """
Click *Yes* if you want to submit the multiple jobs per protocol to a Queue system.
The queue commands for launch and stop jobs should be configured
for the current host in the _hosts.conf_ file.
"""
HELP_WAIT_FOR = """
Specify a comma separated list of protocol IDs if you want
to *schedule* this protocol and wait for those protocols to finish before
starting this one.
This function will allow you to "schedule" many
runs that will be executed after each other.
See %s for more information.
"""
TITLE_NAME_RUN = ' Protocol Run: '
TITLE_RUN = 'Run'
TITLE_LABEL = 'Label'
LABEL_OPT_COMMENT = 'Describe your run here...'
TITLE_COMMENT = 'Comment'
LABEL_RUN_MODE_RESUME = 'resume'
LABEL_RUN_MODE_RESTART = 'restart'
TITLE_EXEC = 'Execution'
TITLE_BROWSE_DATA = 'Protocol data'
LABEL_QUEUE_YES = 'Yes'
LABEL_QUEUE_NO = 'No'
LABEL_PARAM_YES = 'Yes'
LABEL_PARAM_NO = 'No'
LABEL_BUTTON_CLOSE = 'Close'
LABEL_BUTTON_SAVE = 'Save'
LABEL_BUTTON_EXEC = 'Execute'
LABEL_BUTTON_VIS = 'Visualize'
LABEL_BUTTON_WIZ = 'Wizard'
LABEL_BUTTON_HELP = 'Help'
LABEL_BUTTON_RETURN = 'Save'
# VARS
VAR_EXEC_HOST = 'hostName'
VAR_EXPERT = 'expertLevel'
VAR_MPI = 'numberOfMpi'
VAR_QUEUE = '_useQueue'
VAR_RUN_NAME = 'runName'
VAR_COMMENT = 'comment'
VAR_RUN_MODE = 'runMode'
VAR_THREADS = 'numberOfThreads'
LABEL_PATTERN = 'Pattern'
TEXT_PATTERN = """\
Pattern (that can include wildcards) of the files to import.
For example:
*data/particles/***.spi*
*~/Micrographs/mic/***.mrc*"""
ERROR_PATTERN_EMPTY = 'The *pattern* cannot be empty.'
ERROR_PATTERN_FILES = 'There are no files matching the *pattern*'
LABEL_CHECKSTACK = 'Check stack files?'
LABEL_COPYFILES = 'Copy files?'
LABEL_VOLTAGE = 'Microscope voltage (kV)'
TEXT_VOLTAGE = "Microscope voltage"
LABEL_SPH_ABERRATION = 'Spherical aberration (mm)'
TEXT_SPH_ABERRATION = """\
Optical effect due to the increased refraction of light rays when they
strike the lens near its edge, in comparison with those that strike near
the center."""
LABEL_AMPLITUDE = 'Amplitude Contrast'
TEXT_AMPLITUDE = """\
Produced by the loss of amplitude (i.e. electrons) from the beam.
For a weak phase and weak amplitude object, the amplitude contrast ratio Qo
is automatically computed. It should be a positive number, typically between
0.05 and 0.3."""
LABEL_PATTERNU = 'Pattern untilted'
LABEL_PATTERNT = 'Pattern tilted'
LABEL_SAMP_MODE = 'Sampling rate mode'
TEXT_SAMP_MODE = """\
You can specify the sampling rate (pixel size) directly from the image
(A/pixel, Ts) or by specifying the magnification rate (M) and the scanner
pixel size (microns/pixel, Tm).
They are related by Ts = Tm / M"""
LABEL_SAMP_MODE_1 = 'From image'
LABEL_SAMP_MODE_2 = 'From scanner'
LABEL_SAMP_RATE = 'Pixel size (sampling rate) Å/px'
TEXT_SAMP_RATE = "Pixel size"
LABEL_MAGNI_RATE = 'Magnification rate'
TEXT_MAGNI_RATE = """\
Electron optical magnification (M). It can be used to compute the Image Pixel
Size ("Sampling Rate") (Ts) using the Scanner Pixel Size (Tm), Ts = Tm / M."""
LABEL_SCANNED = 'Scanned pixel size (microns/px)'
ERROR_IMPORT_VOL = 'importVolumes: There are no filePaths matching the pattern'
LABEL_CTF_ESTI = 'CTF Estimation'
LABEL_INPUT_MIC = 'Input Micrographs'
LABEL_INPUT_PART = 'Input Particles'
LABEL_INPUT_VOLS = 'Input Volumes'
LABEL_INPUT_MOVS = 'Input Movies'
LABEL_ALIG_PART = 'Write aligned particles?'
TEXT_ALIG_PART = 'If set to *Yes*, the alignment will be applied to \n'+'input particles and a new aligned set will be created.'
TEXT_NO_INPUT_MIC = 'No *Input Micrographs* selected.'
TEXT_NO_CTF_READY = 'CTF of *Input Micrographs* not ready yet.'
TEXT_NO_OUTPUT_CO = 'Output coordinates not ready yet.'
ERROR_NO_EST_CTF = '_estimateCTF should be implemented'
TEXT_NO_OUTPUT_FILES = 'No output file produced'
TITLE_LAUNCHED = 'Success'
LABEL_LAUNCHED = 'The protocol was launched successfully.'
LABEL_FOUND_ERROR = 'Errors found'
TITLE_SAVED_FORM = 'Success'
LABEL_SAVED_FORM = 'The protocol was saved successfully.'
TITLE_DELETE_FORM = 'Confirm DELETE'
TITLE_RESTART_FORM = 'Confirm RESTART'
LABEL_DELETE_FORM = """
You are going to *DELETE* the run(s):
- %s
*ALL DATA* related will be permanently removed.
Do you really want to continue?'
"""
LABEL_RESTART_FORM = """
You are going to *RESTART* the run:
%s
Do you really want to restart it?'
"""
LABEL_RESTART_FORM_MANY = """
Following data will be *REMOVED* :
%s
What do you want to restart?
*Single* : Just this protocol, rest will be reset.
*All*: All above listed protocols will be restarted.
"""
TITLE_STOP_FORM = 'Confirm STOP'
LABEL_STOP_FORM = 'Do you really want to *STOP* this run?'
NO_VIEWER_FOUND = 'There is no viewer for protocol:'
TITLE_SAVE_OUTPUT = 'Save protocol output'
LABEL_SAVE_OUTPUT = 'Do you wish to save protocol output?'
TITLE_RESTART_WORKFLOW_FORM = 'Confirm RESTART'
TITLE_STOP_WORKFLOW_FORM = 'Confirm STOP'
TITLE_RESET_WORKFLOW_FORM = 'Confirm RESET'
TITLE_RESTART_WORKFLOW = 'Do you really want to *RESTART* this Workflow? All previous results will be deleted'
TITLE_STOP_WORKFLOW = 'Do you really want to *STOP* this Workflow?'
TITLE_RESET_WORKFLOW = 'Do you really want to *RESET* this Workflow?'
TITLE_LAUNCHED_WORKFLOW_FAILED_FORM = 'Error while launching the workflow'
TITLE_STOPPED_WORKFLOW_FAILED = 'Error while stopping the workflow'
TITLE_RESETED_WORKFLOW_FAILED = 'Error while resetting the workflow'
TITLE_LAUNCHED_WORKFLOW_FAILED = 'The workflow can not be relaunched from this protocol.\n'
TITLE_ACTIVE_PROTOCOLS = 'The following protocols are active:'
# SHOWJ_WEB
SHOWJ_TITLE = 'Showj'
LABEL_RESLICE = 'Reslice'
RESLICE_Z_NEGATIVE = 'Z Negative (Front)'
RESLICE_Y_NEGATIVE = 'Y Negative (Top)'
RESLICE_Y_POSITIVE = 'Y Positive (Bottom)'
RESLICE_X_NEGATIVE = 'X Negative (Left)'
RESLICE_X_POSITIVE = 'X Positive (Right)'
LABEL_COLS = 'Cols'
LABEL_ROWS = 'Rows'
LABEL_MIRRORY = 'Invert Y Axis'
LABEL_APPLY_TRANSFORM = 'Apply Transform Matrix'
LABEL_ONLY_SHIFTS = 'Only Shifts'
LABEL_WRAP = 'Wrap'
LABEL_BLOCK_SELECTION = 'Select Block'
LABEL_LABEL_SELECTION = 'Select Label'
LABEL_VOLUME_SELECTION = 'Select Volume'
LABEL_ENABLE = 'Enable'
LABEL_DISABLE = 'Disable'
LABEL_SELECT_ALL = 'Select all'
LABEL_SELECT_FROM = 'Select from here'
LABEL_SELECT_TO = 'Select to here'
LABEL_DISPLAY_TABLE_CONFIG = 'Display Table Configuration'
LABEL_LABEL = 'Label'
LABEL_VISIBLE = 'Visible'
LABEL_RENDER = 'Render'
LABEL_BUTTON_OK = 'Ok'
LABEL_BUTTON_CANCEL = 'Cancel'
LABEL_THRESHOLD = 'Threshold:'
ERROR_DIMENSIONS = 'Incorrect table width or height: '
ERROR_WEBGL = 'Your web browser does not support or is not configured for WebGL. See [[http://get.webgl.org/][WebGL Support]] for more information.'
TOOLTIP_SEARCH = 'Search for a given world in the text. '
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>'
TOOLTIP_REFRESH = 'Reload the content of the files in the viewer. '
TOOLTIP_EXTERNAL = 'Open the viewer in an external window. '
TITLE_PICK_GAUSS = 'Automatic gaussian picking'
LABEL_PICK_GAUSS = 'Do you wish to perform an automatic gaussian picking for the remaining micrographs?'
TITLE_INSPECTOR = 'Objects inspector'
LABEL_INSPECTOR = 'Objects inspector will inspect the whole project. ' \
'Thus, it can take a while depending on the size of the project.\n' \
'Do you want to continue?'
EXECUTE_PLUGINS_MANAGER_OPERATION = 'Execute all selected operations'
CANCEL_SELECTED_OPERATION = 'Cancel a selected operation'
# PLUGIN/BINARY STATES
[docs]class PluginStates:
PLUGIN = 'plugin'
BINARY = 'binary'
UNCHECKED = 'unchecked'
CHECKED = 'checked'
INSTALL = 'install'
UNINSTALL = 'uninstall'
TO_INSTALL = 'to_install'
INSTALLED = 'installed'
PRECESSING = 'processing'
FAILURE = 'failure'
AVAILABLE_RELEASE = 'available_release'
TO_UPDATE = 'to_update'
SUCCESS = 'success'
ERRORS = 'errors'
WAITING = 'waiting'
# To get font awesome icons into png use: http://fa2png.io/
[docs]class Icon:
# Protocols status
PROT_DISABLED = 'prot_disabled.png'
BETA = 'beta.png'
NEW = 'new.png'
PRODUCTION = 'production.png'
UPDATED = 'updated.png'
GROUP = 'class_obj.png'
DEBUG = 'debug.png'
DOWNLOAD = 'fa-download.png'
FILE_BW = 'fa-file-o.png'
FIND = 'binoculares.png'
SELECT_ALL = 'workflow.png'
ERROR = 'fa-times-circle_alert.png'
INFO = 'fa-info-circle_alert.png'
ALERT = 'fa-exclamation-triangle_alert.png'
JAVA_FILE = 'file_java.png'
PYTHON_FILE = 'file_python.png'
# Project window icons
RUNS_TREE = 'fa-sitemap.png'
ACTION_NEW = 'fa-plus-circle.png'
ACTION_EDIT = 'fa-pencil.png'
ACTION_SELECT_FROM = 'fa-arrow-down.png'
ACTION_SELECT_TO = 'fa-arrow-up.png'
ACTION_COPY = 'clipboard-regular.png'
ACTION_PASTE = 'paste-solid.png'
ACTION_DUPLICATE = 'fa-files-o.png'
ACTION_DELETE = 'fa-trash-o.png'
ACTION_REFRESH = 'fa-refresh.png'
ACTION_RENAME = 'rename.png'
ACTION_STEPS = 'fa-list-ul.png'
ACTION_BROWSE = 'fa-folder-open.png'
ACTION_DB = 'fa-database.png'
ACTION_TREE = None
ACTION_STOP = 'fa-stop.png'
ACTION_CONTINUE = 'fa-play-circle-o.png'
ACTION_STOP_WORKFLOW = 'fa-stop-workflow.png'
ACTION_RESULTS = 'fa-eye.png'
ACTION_CLOSE = 'fa-times.png'
ACTION_SAVE = 'fa-save.png'
ACTION_VISUALIZE = 'fa-eye.png'
ACTION_WIZ = 'fa-magic.png'
ACTION_HELP = 'fa-question-circle.png'
ACTION_REFERENCES = 'fa-external-link.png'
ACTION_EXPORT = 'fa-external-link.png'
ACTION_EXPORT_UPLOAD = 'fa-upload.png'
ACTION_SEARCH = 'fa-search.png'
ACTION_EXECUTE = 'fa-cogs.png'
ACTION_IN = 'fa-sign-in.png'
ACTION_OUT = 'fa-sign-out.png'
ACTION_FIND_NEXT = 'fa-next.png'
ACTION_FIND_PREVIOUS = 'fa-previous.png'
ACTION_COLLAPSE = 'fa-minus-square.png'
ACTION_EXPAND ='fa-plus-square.png'
# Host template
BUTTON_SELECT = 'fa-check.png'
BUTTON_CLOSE = 'fa-times.png'
BUTTON_CANCEL = 'fa-ban.png'
BUTTON_SAVE = ACTION_SAVE
ARROW_UP = 'fa-arrow-up.png'
TAGS = 'fa-tags.png'
HOME = 'fa-home.png'
LIGHTBULB = 'fa-lightbulb-o.png'
PLUS_CIRCLE = 'fa-plus-circle.png'
ROCKET = 'fa-rocket.png'
NO_IMAGE_128 = 'no-image128.png'
FOLDER = 'file_folder.png'
FOLDER_LINK = 'file_folder_link.png'
FILE = 'file_generic.png'
FILE_LINK = 'file_generic_link.png'
FOLDER_OPEN = 'fa-folder-open.png'
DB = 'file_sqlite.png'
TXT_FILE = 'file_text.png'
POWER_OFF = 'power-off-solid.png'
BROOM = 'broom-solid.png'
BACKWARD = 'backward-solid.png'
CODE_BRANCH = 'code-branch-solid.png'
SCIPION_ICON = 'scipion_icon.png'
SCIPION_ICON_PROJ = SCIPION_ICON # 'scipion_icon_proj.png'
SCIPION_ICON_PROJS = SCIPION_ICON # 'scipion_icon_projs.png'
SCIPION_ICON_PROT = SCIPION_ICON # 'scipion_icon_prot.png'
# PLUGIN MANAGER ICONS
CHECKED = 'fa-checked.png'
UNCHECKED = 'fa-unchecked.png'
INSTALL = 'fa-install.png'
UNINSTALL = 'fa-uninstall.png'
TO_INSTALL = 'fa-to_install.png'
INSTALLED = 'fa-installed.png'
PROCESSING = 'fa-processing.png'
FAILURE = 'fa-failure.png'
DELETE_OPERATION = 'fa-delete-operation.png'
TO_UPDATE = 'fa-update.png'
WAITING = 'wait.gif'
ACTION_UNDO = 'fa-undo.png'
PLUGIN_AUTHORS = 'users.png'
PLUGIN_DESCRIPTION = 'file_stack.png'
PLUGIN_RELEASE_DATE = 'fa-upload.png'
PLUGIN_VERSION = 'file_vol.png'
PLUGIN_PACKAGE = 'file_folder.png'
[docs]class colorText:
"""printing in colors, bold, etc,
example: print colorText.BOLD + 'Hello World !' + color.END
"""
PURPLE = '\033[95m'
CYAN = '\033[96m'
DARKCYAN = '\033[36m'
BLUE = '\033[94m'
GREEN = '\033[92m'
YELLOW = '\033[93m'
RED = '\033[91m'
BOLD = '\033[1m'
UNDERLINE = '\033[4m'
END = '\033[0m'
[docs]class KEYSYM:
""" 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'