# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
# *
# * 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, see <https://www.gnu.org/licenses/>.
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
import csv
import os
import re
from pwem.objects import SetOfClasses2D
from pyworkflow.config import Config as pwConfig
from pyworkflow.gui import getDefaultFont, openTextFileEditor
import tkinter as tk
import tkinter.ttk as ttk
import pyworkflow.viewer as pwviewer
from pwem import emlib
from .showj import (getJvmMaxMemory, MODE, VISIBLE, ZOOM, ORDER, RENDER,
SORT_BY, runJavaIJapp, MODE_MD, LABELS,
launchSupervisedPickerGUI)
[docs]class DataView(pwviewer.View):
""" Wrapper the arguments to showj (either web or desktop).
Also useful to visualize images that are not objects,
e.g.: dark or gain images"""
def __init__(self, path, viewParams={}, **kwargs):
pwviewer.View.__init__(self)
self._memory = getJvmMaxMemory()
self._loadPath(path)
self._env = kwargs.get('env', {})
self._viewParams = viewParams
[docs] def setMemory(self, memory):
self._memory = memory
[docs] def getViewParams(self):
""" Give access to the viewParams dict. """
return self._viewParams
def _loadPath(self, path):
self._tableName = None
# If path is a tuple, we will convert to the filename format
# as expected by Showj
if isinstance(path, tuple):
self._path = emlib.image.ImageHandler.locationToXmipp(path)
# Check if there is a table name with @ in path
# in that case split table name and path
# table names can never starts with a number
# this is considering an image inside an stack
elif isinstance(path, str):
if '@' in path and path[0] not in '0123456789':
self._tableName, self._path = path.split('@')
else:
self._path = path
else:
raise Exception("Invalid input path, "
"should be 'string' or 'tuple'")
[docs] def show(self):
runJavaIJapp(self._memory,
'xmipp.viewer.scipion.ScipionViewer',
self.getShowJParams(), env=self._env)
[docs] def getShowJParams(self):
tableName = '%s@' % self._tableName if self._tableName else ''
params = '-i "%s%s"' % (tableName, self._path)
for key, value in self._viewParams.items():
params = "%s --%s %s" % (params, key, value)
if pwConfig.debugOn():
params += " --debug"
return params
[docs] def getShowJWebParams(self):
parameters = {
MODE, # FOR MODE TABLE OR GALLERY
VISIBLE,
ZOOM,
ORDER,
RENDER,
SORT_BY
}
params = {}
for key, value in self._viewParams.items():
if key in parameters:
if key == 'mode' and value == 'metadata':
value = 'table'
params[key] = value
return params
[docs] def getPath(self):
return self._path
[docs] def getTableName(self):
return self._tableName
[docs]class ObjectView(DataView):
""" Wrapper to DataView but for displaying Scipion objects. """
def __init__(self, project, inputid, path, other='', viewParams={},
**kwargs):
DataView.__init__(self, path, viewParams, **kwargs)
self.type = type
self.port = project.port
self.inputid = inputid
self.other = other
[docs] def getShowJParams(self):
# Add the scipion parameters over the normal showj params
return '%s --scipion %s %s %s' % (DataView.getShowJParams(self),
self.port, self.inputid, self.other)
[docs] def show(self):
runJavaIJapp(self._memory, 'xmipp.viewer.scipion.ScipionViewer',
self.getShowJParams(), env=self._env)
[docs]class MicrographsView(ObjectView):
""" Customized ObjectView for SetOfCTF objects . """
# All extra labels that we want to show if present in the CTF results
RENDER_LABELS = ['thumbnail._filename', 'psdCorr._filename',
'plotGlobal._filename']
EXTRA_LABELS = ['_filename']
def __init__(self, project, micSet, other='', **kwargs):
first = micSet.getFirstItem()
def existingLabels(labelList):
return ' '.join([l for l in labelList if first.hasAttributeExt(l)])
renderLabels = existingLabels(self.RENDER_LABELS)
extraLabels = existingLabels(self.EXTRA_LABELS)
labels = 'id enabled %s %s' % (renderLabels, extraLabels)
viewParams = {MODE: MODE_MD,
ORDER: labels,
VISIBLE: labels,
ZOOM: 50
}
if renderLabels:
viewParams[RENDER] = renderLabels
inputId = micSet.getObjId() or micSet.getFileName()
ObjectView.__init__(self, project,
inputId, micSet.getFileName(), other,
viewParams, **kwargs)
[docs]class CtfView(ObjectView):
""" Customized ObjectView for SetOfCTF objects . """
# All extra labels that we want to show if present in the CTF results
PSD_LABELS = ['_micObj.thumbnail._filename', '_psdFile',
'_xmipp_enhanced_psd', '_xmipp_ctfmodel_quadrant',
'_xmipp_ctfmodel_halfplane', '_micObj.plotGlobal._filename'
]
EXTRA_LABELS = ['_ctftilt_tiltAxis', '_ctftilt_tiltAngle',
'_xmipp_ctfCritFirstZero',
'_xmipp_ctfCritCorr13', '_xmipp_ctfCritIceness', '_xmipp_ctfCritFitting',
'_xmipp_ctfCritNonAstigmaticValidty',
'_xmipp_ctfCritCtfMargin', '_xmipp_ctfCritMaxFreq',
'_xmipp_ctfCritPsdCorr90', '_xmipp_ctfVPPphaseshift'
]
def __init__(self, project, ctfSet, other='', **kwargs):
first = ctfSet.getFirstItem()
def existingLabels(labelList):
return ' '.join([l for l in labelList if first.hasAttributeExt(l)])
psdLabels = existingLabels(self.PSD_LABELS)
extraLabels = existingLabels(self.EXTRA_LABELS)
labels = 'id enabled %s _defocusU _defocusV ' % psdLabels
labels += '_defocusAngle _defocusRatio '
labels += '_phaseShift _resolution _fitQuality %s ' % extraLabels
labels += ' _micObj._filename'
viewParams = {MODE: MODE_MD,
ORDER: labels,
VISIBLE: labels,
ZOOM: 50
}
if psdLabels:
viewParams[RENDER] = psdLabels
if ctfSet.isStreamOpen():
viewParams['dont_recalc_ctf'] = ''
inputId = ctfSet.getObjId() or ctfSet.getFileName()
ObjectView.__init__(self, project,
inputId, ctfSet.getFileName(), other,
viewParams, **kwargs)
[docs]class ClassesView(ObjectView):
""" Customized ObjectView for SetOfClasses. """
def __init__(self, project, inputid, path, other='',
viewParams={}, **kwargs):
from pwem.viewers.viewers_data import RegistryViewerConfig
config = RegistryViewerConfig.getConfig(SetOfClasses2D)
defaultViewParams = config.copy()
defaultViewParams.update(viewParams)
ObjectView.__init__(self, project, inputid, path, other,
defaultViewParams, **kwargs)
[docs]class Classes3DView(ClassesView):
""" Customized ObjectView for SetOfClasses. """
def __init__(self, project, inputid, path, other='',
viewParams={}, **kwargs):
defaultViewParams = {ZOOM: '99',
MODE: 'metadata'}
defaultViewParams.update(viewParams)
ClassesView.__init__(self, project, inputid, path, other,
defaultViewParams, **kwargs)
[docs]class CoordinatesObjectView(DataView):
""" Wrapper to View but for displaying Scipion objects. """
MODE_AUTOMATIC = 'Automatic'
def __init__(self, project, path, outputdir, protocol, pickerProps=None,
inTmpFolder=False, **kwargs):
DataView.__init__(self, path, **kwargs)
self.project = project
self.outputdir = outputdir
self.protocol = protocol
self.pickerProps = pickerProps
self.inTmpFolder = inTmpFolder
self.mode = kwargs.get('mode', None)
[docs] def show(self):
return launchSupervisedPickerGUI(self._path, self.outputdir,
self.protocol, mode=self.mode,
pickerProps=self.pickerProps,
inTmpFolder=self.inTmpFolder)
[docs]class ImageView(pwviewer.View):
""" Customized ObjectView for SetOfClasses. """
def __init__(self, imagePath, **kwargs):
pwviewer.View.__init__(self)
self._imagePath = os.path.abspath(imagePath)
[docs] def getImagePath(self):
return self._imagePath
[docs]class TableView(pwviewer.View):
""" show table, pass values as:
headerList = ['name', 'surname']
dataList = [
('John', 'Smith') ,
('Larry', 'Black') ,
('Walter', 'White') ,
('Fred', 'Becker')
].
msg = message to be shown at the table top
title= window title
height: Specifies the number of rows which should be visible
width: minimum width in pixels
fontSize= font size
padding: cell extra width
---------------------
Alternative way to create a table using showj
views = []
labels = '_1 _2'
emSet = EMSet(filename="/tmp/kk.sqlite")
emObject = EMObject()
emObject._1 = String('first parameter')
emObject._2 = Float(12.)
emSet.append(emObject)
emObject = EMObject()
emObject._1 = String('second parameter')
emObject._2 = Float(22.)
emSet.append(emObject)
emSet.write()
views.append(ObjectView(self._project,
self.protocol.strId(),
"/tmp/kk.sqlite",
viewParams = {MODE: MODE_MD, ORDER: labels,
VISIBLE: labels}))
return views
"""
def __init__(self, headerList, dataList,
mesg=None, title=None,
height=10, width=400,
padding=10, outFileName=None):
"""Get new widget that has as parent the top level window and set title.
tables can be dump to a csv file. The name of the file is outFileName
"""
self.title = title
self.headerList = headerList
self.dataList = dataList
self.outFileName = outFileName
win = tk.Toplevel()
if title:
win.wm_title(title)
# frame to place all other widgets
frame = tk.Frame(win)
font = getDefaultFont()
font.metrics()
fontheight = font.metrics()['linespace']
style = ttk.Style()
style.configure('Calendar.Treeview', font=font, rowheight=fontheight)
# add a "save data" button
saveDataButton = ttk.Button(master=win, text="Save Data",
command=self.saveData)
# create treeview to store multi list with data
tree = ttk.Treeview(columns=headerList,
show="headings", master=win,
style='Calendar.Treeview', height=height
)
# define scrollbars to be added
if len(dataList) > height:
ysb = ttk.Scrollbar(orient=tk.VERTICAL, command=tree.yview,
master=win)
# xsb = ttk.Scrollbar(orient=tk.HORIZONTAL,
# command= tree.xview, master=win)
# add them to three view
tree.configure(yscroll=ysb.set) # , xscroll=xsb.set)
# create rows and columns
counterRow = 1
colWidths = [] # list with maximum width per column
# create headers
for col in headerList:
tree.heading(col, text=col.title())
# save neede width for this cell
(w, h) = (font.measure(col.title()), font.metrics("linespace"))
colWidths.append(w)
# insert other rows
# tag rows as odd or even so they may have different background colors
for item in dataList:
if counterRow % 2:
tree.insert('', 'end', values=item, tags=('evenrow',))
else:
tree.insert('', 'end', values=item, tags=('oddrow',))
counterRow += 1
counterCol = 0
for i in item:
(w, h) = (font.measure(i), font.metrics("linespace"))
if colWidths[counterCol] < w:
colWidths[counterCol] = w
counterCol += 1
# if width less than sum of column widths expand them
sumColWid = sum(colWidths) + 20
if sumColWid < width:
sumColWid = width
factor = int(width / sumColWid) + 1
colWidths = [i * factor for i in colWidths]
for col, colWidth in zip(headerList, colWidths):
tree.column(col, width=colWidth + padding)
# color by rows
tree.tag_configure('evenrow', background='white')
tree.tag_configure('oddrow', background='light grey')
# message placed at the window top
msg = ttk.Label(wraplength=sumColWid, justify="left", anchor="n",
padding=(10, 2, 10, 6), text=mesg, master=win,
font=font)
# set mg in grid 0,0
msg.grid(row=0, column=0)
# set button in grid 1 0
saveDataButton.grid(row=1, column=0)
# set ysg in grid 2 0
tree.grid(row=2, column=0)
# set ysg in grid 2 1
# but only if number of elements is larger than height
if len(dataList) > height:
ysb.grid(row=2, column=1, sticky='ns')
[docs] def saveData(self):
""" Save data in the treeView Widget to a file.
If not provided the outfile is in the Logs directory
the name is the title of the table"""
def slugify(value):
"""
Create a valid file name from the table title.
Normalizes string, converts to lowercase, removes non-alpha characters,
and converts spaces to hyphens.
"""
value = re.sub('[^\w\s-]', '', value).strip().lower()
value = re.sub('[-\s]+', '-', value)
return value
if self.outFileName is None:
outFileName = slugify(self.title) + ".csv"
outFileName = os.path.join(os.getcwd(), 'Logs', outFileName)
print("Data saved to file: ", outFileName)
with open(outFileName, "wt") as f:
f.write("# TITLE = %s\n" % self.title)
spamWriter = csv.writer(f)
spamWriter.writerow(self.headerList)
for data in self.dataList:
spamWriter.writerow(data)
f.close()
# call the application used to handle csv files.
openTextFileEditor(outFileName)