class SaveLoadTab(object):
"""The tab that lets the user FileSelect
a file to open or to save.
"""
def __init__(self, parent, frame):
"""Init. args: parent: the guiElement that this
tab is part of.
frame: the frame this part of the
GUI lives in.
"""
self.guiParent = parent
self.frame = frame
self.project = parent.project
self.nmrProject = parent.nmrProject
self.loadAndSaveButtons = None
self.fileselectionBox = None
self.body()
def body(self):
"""Setting up the body of this view."""
frame = self.frame
file_types = [FileType("pyc", ["*.pyc"])]
self.fileselectionBox = FileSelect(frame, multiSelect=False, file_types=file_types)
self.fileselectionBox.grid(row=0, column=0, columnspan=6, sticky="nsew")
texts = ["Load", "Save"]
commands = [self.loadDataFromPyc, self.saveDataToPyc]
self.loadAndSaveButtons = ButtonList(frame, commands=commands, texts=texts)
self.loadAndSaveButtons.grid(row=1, column=0, sticky="nsew")
frame.grid_rowconfigure(0, weight=1)
frame.grid_columnconfigure(0, weight=1)
def saveDataToPyc(self):
"""Save the data to the selected file."""
if self.guiParent.connector.results:
fileName = self.fileselectionBox.getFile()
self.guiParent.connector.saveDataToPyc(fileName)
self.fileselectionBox.updateFileList()
else:
string = """There are no results to save, """ """the algorithm has not run yet."""
showWarning("No Results to Save", string, parent=self.guiParent)
def loadDataFromPyc(self):
"""Load the data from the selected file."""
fileName = self.fileselectionBox.getFile()
self.guiParent.connector.loadDataFromPyc(fileName)
self.guiParent.resultsTab.update()
class OpenProjectPopup(BasePopup):
def __init__(self,
parent,
title='Project : Open',
callback=None,
help_msg='',
help_url='',
load_project=None,
*args,
**kw):
self.callback = callback
self.help_msg = help_msg
self.help_url = help_url
self.project = None
if not load_project:
askdir = lambda title, prompt, initial_value: askDir(
title,
prompt,
initial_value,
parent=self,
extra_dismiss_text='Skip')
askfile = lambda title, prompt, initial_value: askFile(
title,
prompt,
initial_value,
parent=self,
extra_dismiss_text='Skip')
load_project = lambda path: loadProject(
path, showWarning=showWarning, askDir=askdir, askFile=askfile)
self.load_project = load_project
BasePopup.__init__(self, parent=parent, title=title, *args, **kw)
def body(self, master):
self.geometry('600x500')
master.grid_rowconfigure(1, weight=1)
master.grid_columnconfigure(0, weight=1)
label = Label(master, text='Select Project Directory')
label.grid(row=0, column=0, sticky=Tkinter.W)
file_types = [FileType('Project', ['*.xml']), FileType('All', ['*'])]
self.file_select = FileSelect(master,
file_types=file_types,
show_file=False,
double_callback=self.ok,
getRowColor=self.getEntryColor,
getExtraCell=self.getProjectFileText,
extraHeadings=('Status', ),
extraJustifies=('left', ))
self.file_select.grid(row=1, column=0, sticky=Tkinter.NSEW)
texts = ['Open']
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Cancel',
help_msg=self.help_msg,
help_url=self.help_url)
buttons.grid(row=2, column=0, sticky=Tkinter.EW)
self.ok_button = buttons.buttons[0]
def getEntryColor(self, fileName):
# this function returns background color for entry
if doesRepositoryContainProject(fileName):
color = '#C0FFC0' # green
elif getPossibleProjectFiles(fileName):
color = '#FFFFC0' # yellow
else:
color = None # default
return color
def getProjectFileText(self, fileName):
if doesRepositoryContainProject(fileName):
tt = time.localtime(os.path.getmtime(fileName))
tt = '%4d-%02d-%02d %02d:%02d:%02d' % tt[:6]
data = 'OK (%s)' % tt
else:
files = getPossibleProjectFiles(fileName)
nfiles = len(files)
if nfiles == 1:
data = '%s' % os.path.basename(files[0])
elif nfiles:
data = '%d possible' % nfiles
else:
data = None
data = (data, )
return data
def disableOk(self):
self.file_select.double_callback = None
self.ok_button.config(state=Tkinter.DISABLED)
def enableOk(self):
self.file_select.double_callback = self.ok
self.ok_button.config(state=Tkinter.NORMAL)
def apply(self):
# protect against repeated double-clicking
if (self.project):
return False
path = self.file_select.getDirectory()
if not doesRepositoryContainProject(
path) and not getPossibleProjectFiles(path):
self.file_select.changeDir(path)
return False
self.disableOk()
self.project = None
if not path:
showError('No path', 'Need to select path', self)
self.enableOk()
return False
try:
self.project = self.load_project(path)
except ApiError, e:
showError('Loading project', e.error_msg, self)
self.enableOk()
return False
except IOError, e:
showError('Loading project', str(e), self)
self.enableOk()
return False
class FormatFilePopup(BasePopup):
def __init__(self,
parent,
file=None,
files=None,
component=None,
selectionText='Select',
title=None,
format=None,
multiSelect=False):
#
# Also get format (from self?)
#
self.file = None # Use this to return single file info, for backward compat
if not multiSelect and file:
self.files = [file]
elif files:
self.files = files
else:
self.files = []
if self.files:
for i in range(len(self.files)):
self.files[i] = normalisePath(self.files[i])
self.component = component
self.fileSelected = False
self.selectionText = selectionText
self.format = format
self.multiSelect = multiSelect
if not title:
title = 'Select %s file' % component
BasePopup.__init__(self,
parent=parent,
title=title,
modal=True,
transient=True)
def body(self, master):
master.grid_columnconfigure(0, weight=1)
master.grid_rowconfigure(0, weight=1)
master.grid_rowconfigure(1, weight=1)
self.geometry('500x500')
fileNames = []
# All files have to be in same directory!
if self.files and self.files[0].find(dirsep) > -1:
(path, fileName) = splitPath(self.files[0])
directory = path
fileNames.append(fileName)
for file in self.files[1:]:
(path, fileName) = splitPath(file)
fileNames.append(fileName)
else:
path = None
directory = normalisePath(os.path.abspath(os.curdir))
fileNames = []
#print directory
#print fileName
file_types = []
if fileTypeDict.has_key(self.component):
if self.format and fileTypeDict[self.component].has_key(
self.format):
file_types.extend([
FileType(self.format,
fileTypeDict[self.component][self.format])
])
if fileTypeDict[self.component].has_key('generic'):
file_types.extend([
FileType('generic',
fileTypeDict[self.component]['generic'])
])
file_types.extend([FileType('All', ['*'])])
self.file_select = FileSelect(master,
file_types=file_types,
directory=directory,
double_callback=self.ok,
multiSelect=self.multiSelect)
if self.multiSelect:
self.file_select.setFiles(fileNames)
else:
if fileNames:
fileName = fileNames[0]
else:
fileName = ''
self.file_select.setFile(fileName)
self.file_select.grid(row=0, column=0, sticky=Tkinter.NSEW)
texts = [self.selectionText]
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands)
buttons.grid(row=1, column=0, sticky=Tkinter.EW)
def apply(self):
if not self.multiSelect:
file = self.file_select.getFile()
if file:
files = [file]
else:
files = []
else:
files = self.file_select.getFiles()
if (not files):
self.files = None
return False
self.fileSelected = True
self.files = []
# Handle symbolic links in Linux/unix
for file in files:
symbolicLinkIndex = string.find(file, '->')
if symbolicLinkIndex != -1:
self.files.append(file[symbolicLinkIndex + 3:])
else:
self.files.append(file)
# For single files, set self.file for backward compat
if not self.multiSelect:
self.file = self.files[0]
return True
class SaveLoadTab(object):
'''The tab that lets the user FileSelect
a file to open or to save.
'''
def __init__(self, parent, frame):
'''Init. args: parent: the guiElement that this
tab is part of.
frame: the frame this part of the
GUI lives in.
'''
self.guiParent = parent
self.frame = frame
self.project = parent.project
self.nmrProject = parent.nmrProject
self.loadAndSaveButtons = None
self.fileselectionBox = None
self.body()
def body(self):
'''Setting up the body of this view.'''
frame = self.frame
file_types = [FileType('pyc', ['*.pyc'])]
self.fileselectionBox = FileSelect(frame,
multiSelect=False,
file_types=file_types)
self.fileselectionBox.grid(row=0,
column=0,
columnspan=6,
sticky='nsew')
texts = ['Load', 'Save']
commands = [self.loadDataFromPyc, self.saveDataToPyc]
self.loadAndSaveButtons = ButtonList(frame,
commands=commands,
texts=texts)
self.loadAndSaveButtons.grid(row=1, column=0, sticky='nsew')
frame.grid_rowconfigure(0, weight=1)
frame.grid_columnconfigure(0, weight=1)
def saveDataToPyc(self):
'''Save the data to the selected file.'''
if self.guiParent.connector.results:
fileName = self.fileselectionBox.getFile()
self.guiParent.connector.saveDataToPyc(fileName)
self.fileselectionBox.updateFileList()
else:
string = ('''There are no results to save, '''
'''the algorithm has not run yet.''')
showWarning('No Results to Save', string, parent=self.guiParent)
def loadDataFromPyc(self):
'''Load the data from the selected file.'''
fileName = self.fileselectionBox.getFile()
self.guiParent.connector.loadDataFromPyc(fileName)
self.guiParent.resultsTab.update()
class ArchiveProjectPopup(BasePopup):
"""
**Archive the Project**
This popup window enables the user to archive the CCPN Project into a gzipped
tar file. By default it only includes the *.xml files which reside in the
project directory. If the "Include *.xml.bak files" check button is checked
then it will also include the *.xml.bak files which reside in the project
directory. If the "Include data files which are in the project directory"
check button is checked then it will also include the binary data files
which reside in the project directory.
**Caveats & Tips**
The archive excludes the reference data *.xml files (quite sensibly).
"""
def __init__(self,
parent,
project,
title='Project : Archive',
callback=None,
help_msg='',
help_url='',
dismiss_text='',
*args,
**kw):
self.callback = callback
self.help_msg = help_msg
self.help_url = help_url
self.dismiss_text = dismiss_text
BasePopup.__init__(self,
parent=parent,
project=project,
title=title,
*args,
**kw)
def body(self, guiParent):
now = datetime.date.today().strftime('%y%m%d')
filePrefix = '%s_%s' % (self.project.name, now)
projDir = getUserDataPath(self.project)
directory = os.path.dirname(projDir)
guiParent.grid_rowconfigure(0, weight=1)
guiParent.grid_columnconfigure(1, weight=1)
row = 0
label = Label(guiParent, text='Archive File:')
label.grid(row=row, column=0, sticky=Tkinter.E)
tipText = 'File name (excluding .tgz ending) for archive'
self.fileEntry = Entry(guiParent, text=filePrefix, tipText=tipText)
self.fileEntry.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(guiParent, text='.tgz (automatically appended)')
label.grid(row=row, column=2, sticky=Tkinter.W)
row = row + 1
self.backupCheck = CheckButton(
guiParent,
text='Include *.xml.bak files',
tipText='If checked include *.xml.bak files')
self.backupCheck.grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
self.dataCheck = CheckButton(
guiParent,
text='Include data files which are in project directory',
tipText=
'If checked include data files if they are located in project directory'
)
self.dataCheck.grid(row=row, column=1, columnspan=2, sticky=Tkinter.W)
row = row + 1
labelFrame = LabelFrame(guiParent, text='Archive Location')
labelFrame.grid(row=row, column=0, columnspan=3, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(0, weight=1)
self.dirSelect = FileSelect(labelFrame,
directory=directory,
show_file=False)
self.dirSelect.grid(row=0, column=0, sticky=Tkinter.NSEW)
guiParent.grid_rowconfigure(row, weight=1)
row = row + 1
texts = ['Save']
tipTexts = ['Create archive file']
commands = [self.save]
buttons = createDismissHelpButtonList(guiParent,
texts=texts,
tipTexts=tipTexts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url,
dismiss_text=self.dismiss_text,
expands=True)
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
def save(self):
filePrefix = self.fileEntry.get()
directory = self.dirSelect.getDirectory()
filePrefix = joinPath(directory, filePrefix)
fileName = filePrefix + '.tgz'
if os.path.exists(fileName):
if not showYesNo('File exists',
'File "%s" exists, overwrite?' % fileName,
parent=self):
return
includeBackups = self.backupCheck.isSelected()
includeData = self.dataCheck.isSelected()
packageProject(self.project, filePrefix, includeBackups, includeData)
class FileSelectPopup(BasePopup):
def __init__(self,
parent,
file_types=None,
directory=None,
multiSelect=False,
title='Browse files',
prompt=None,
show_file=True,
file='',
dismiss_text='Close',
extra_dismiss_text='',
selected_file_must_exist=False,
default_dir=None,
*args,
**kw):
self.file_types = file_types
self.directory = directory
self.prompt = prompt
self.show_file = show_file
self.dismiss_text = dismiss_text
self.extra_dismiss_text = extra_dismiss_text
self.initial_file = file
self.selected_file_must_exist = selected_file_must_exist
self.default_dir = default_dir
self.multiSelect = multiSelect
kw['title'] = title
kw['transient'] = True
kw['modal'] = True
BasePopup.__init__(self, parent=parent, *args, **kw)
def body(self, master):
self.geometry('600x400')
master.grid_rowconfigure(0, weight=1)
master.grid_columnconfigure(0, weight=1)
self.result = ''
self.file_select = FileSelect(master,
file_types=self.file_types,
directory=self.directory,
prompt=self.prompt,
show_file=self.show_file,
file=self.initial_file,
multiSelect=self.multiSelect,
default_dir=self.default_dir)
self.file_select.grid(row=0, column=0, sticky=Tkinter.NSEW)
texts = ['Ok']
commands = [self.ok]
if (self.extra_dismiss_text):
texts.append(self.extra_dismiss_text)
commands.append(self.extra)
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text=self.dismiss_text)
buttons.grid(row=1, column=0, sticky=Tkinter.EW)
def apply(self):
self.result = ''
file = self.file_select.getFile()
if (self.selected_file_must_exist and not os.path.exists(file)):
showError('No file', 'File does not exist', self)
return False
self.result = file
return True
def extra(self):
self.result = None
self.close()
def getFile(self):
if (self.result):
return self.file_select.getFile()
else:
return self.result
def getDirectory(self):
if (self.result):
return self.file_select.getDirectory()
else:
return self.result
def open(self, file=''):
if (file):
self.setFile(file)
BasePopup.open(self)
def __getattr__(self, name):
try:
return getattr(self.__dict__['file_select'], name)
except:
raise AttributeError, "%s instance has no attribute '%s'" % (
self.__class__.__name__, name)
class OpenMacroPopup(BasePopup):
"""
**Locate Python Macro Scripts On Disk**
This popup is used to locate a Python file and function definition on disk
so that it can be loaded into Analysis as a "Macro". The top table
is a file browser that the user can navigate to the location of the Python
file (typically sending in ".py"). When a Python file is selected in the
upper table the system will look through the contents of the file to find
any macro functions that are defined within. Note that a macro function
is defined by the normal Python "def" keyword but must take "argSever"
as its first input argument.
Any macro functions in the selected file will be displayed in the
lower table. Clicking on the name of a function in this table
selects it for opening. The user may edit the name of the macro for
display purposes within Analysis. Finally clicking [Load Macro]
will add it to the CCPN project, stored in a user-specific way
inside the current Analysis profile. Once loaded into the
project the new macro will appear in the main macro table
(the "Macros" tab of `User Options`_)
.. _`User Options`: EditProfilesPopup.html
"""
def __init__(self, parent, **kw):
# TBD: properly
transient = True
BasePopup.__init__(self, parent=parent, title='Open macro', transient=transient, **kw)
def body(self, guiParent):
guiParent.grid_columnconfigure(1,weight=1)
row = 0
file_types = [ FileType('Python', ['*.py']), FileType('All', ['*']) ]
self.file_select = FileSelect(guiParent, file_types=file_types,
single_callback=self.chooseFile,
double_callback=self.chooseFile)
self.file_select.grid(row=row, column=0, columnspan=2, sticky='nsew')
row = row + 1
headingList=('Function',)
self.scrolledMatrix = ScrolledMatrix(guiParent, initialRows=4,
headingList=headingList, callback=self.selectFunction)
self.scrolledMatrix.grid(row=row, column=0, columnspan=2, sticky='nsew')
guiParent.grid_rowconfigure(row,weight=1)
row = row + 1
self.moduleLabel1 = Label(guiParent, text='Module: ')
self.moduleLabel1.grid(row=row, column=0, sticky='nw')
self.moduleLabel2 = Label(guiParent, text=' ')
self.moduleLabel2.grid(row=row, column=1, sticky='nw')
row = row + 1
self.functionLabel1 = Label(guiParent, text='Function: ')
self.functionLabel1.grid(row=row, column=0, sticky='nw')
self.functionLabel2 = Label(guiParent, text=' ')
self.functionLabel2.grid(row=row, column=1, sticky='nw')
row = row + 1
self.nameLabel = Label(guiParent, text='Name: ')
self.nameLabel.grid(row=row, column=0, sticky='nw')
self.nameEntry = Entry(guiParent, text=' ', width=40)
self.nameEntry.grid(row=row, column=1, sticky='nw')
row = row + 1
texts = [ 'Load Macro' ]
commands = [ self.loadMacro ]
buttons = UtilityButtonList(guiParent, texts=texts,
commands=commands, helpUrl=self.help_url)
buttons.grid(row=row, column=0, columnspan=2, sticky='ew')
self.loadButton = buttons.buttons[0]
self.loadButton.disable()
self.path = None
self.module = None
self.function = None
def selectFunction(self, function, row, col):
if function:
self.loadButton.enable()
self.function = function
self.functionLabel2.set(function)
self.nameEntry.set(function)
def updateFunctions(self, file):
self.loadButton.disable()
functions = []
fileHandle = open(file, 'r')
line = fileHandle.readline()
textMatrix = []
while line :
match = re.match('\s*def\s+(\w+)\s*\(.*argServer',line)
if match:
function = match.group(1)
functions.append(function)
textMatrix.append( [function,] )
line = fileHandle.readline()
self.scrolledMatrix.update(objectList=functions,textMatrix=textMatrix)
def chooseFile(self, file):
fullPath =self.file_select.getFile()
if not os.path.isdir(fullPath) and file:
(self.path, module) = splitPath(fullPath)
module = re.sub('\..+?$','',module)
self.module = module
self.moduleLabel2.set(module)
self.updateFunctions(file)
def loadMacro(self):
if self.module and self.function and self.path:
name = self.nameEntry.get()
if not name:
name = self.function
analysisProfile = self.analysisProfile
m1 = analysisProfile.newMacro(name=name,path=self.path,
function=self.function,
module=self.module,ordering=1)
self.close()
class SaveProjectFrame(Frame):
def __init__(self,
guiParent,
project,
callback=None,
help_msg='',
help_url='',
dismiss_text='',
modal=False,
*args,
**kw):
self.project = project
self.callback = callback
self.help_msg = help_msg
self.help_url = help_url
self.dismiss_text = dismiss_text
self.modal = modal
self.did_save = False
Frame.__init__(self, guiParent, *args, **kw)
projDir = Io.getUserDataPath(self.project)
guiParent.grid_columnconfigure(1, weight=1)
row = 0
label = Label(guiParent, text='Project Name:')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.proj_name_entry = Entry(
guiParent,
text=self.project.name,
returnCallback=self.updateInfo,
leaveCallback=self.updateInfo,
tipText='The name used for the project save directory')
self.proj_name_entry.grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
label = Label(guiParent, text='Project Directory:')
label.grid(row=row, column=0, sticky=Tkinter.E)
label = self.proj_dir_label = Label(guiParent, text=projDir)
label.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(
guiParent,
text='Note: Project Directory = Save Location + Project Name')
label.grid(row=row, column=1, sticky=Tkinter.W)
text = 'Save binary data with project'
tipText = 'Copy data files (e.g. for spectra) into new project directory if not already in current project directory: careful, this can take some time'
row = row + 1
self.dataCheckButton = CheckButton(guiParent,
text=text,
tipText=tipText)
self.dataCheckButton.grid(row=row,
column=0,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
guiParent.grid_rowconfigure(row, weight=1)
labelFrame = LabelFrame(guiParent, text='Save Location')
labelFrame.grid(row=row, column=0, columnspan=2, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(0, weight=1)
directory = os.path.dirname(projDir)
self.proj_dir_select = FileSelect(
labelFrame,
directory=directory,
select_dir_callback=self.selectDir,
change_dir_callback=self.updateInfo,
should_change_dir_callback=self.shouldChangeDir,
getRowColor=self.getEntryColor,
show_file=False)
self.proj_dir_select.grid(row=0, column=0, sticky=Tkinter.NSEW)
row = row + 1
texts = ['Save']
tipTexts = ['Save project with specified name in specified directory']
commands = [self.save]
buttons = createDismissHelpButtonList(guiParent,
texts=texts,
tipTexts=tipTexts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url,
dismiss_text=self.dismiss_text,
expands=True)
buttons.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
def save(self):
projName = self.proj_name_entry.get()
directory = self.proj_dir_select.getDirectory()
directory = joinPath(directory, projName)
if self.isProjectDirectory(directory):
if not showOkCancel('Overwrite directory',
'Overwrite existing project directory?',
parent=self):
return
self.updateInfo()
self.did_save = False
changeDataLocations = self.dataCheckButton.isSelected()
done = False
try:
done = Io.saveProject(self.project,
newPath=directory,
newProjectName=projName,
createFallback=True,
showYesNo=showYesNo,
changeDataLocations=changeDataLocations,
showWarning=showWarning)
if done:
showInfo('Project saved', 'Project saved successfully')
self.did_save = True
if self.callback:
self.callback(self.project)
elif self.modal:
return # give another chance
except Implementation.ApiError, e:
showError('Save project', e.error_msg)
except IOError, e:
showError('Save project', str(e))
class OpenSpectrumPopup(BasePopup):
r"""
**Locate Spectrum Data for Use in CCPN Project**
This popup window enables the user to locate spectrum data within a file
system and associate the files (typically binary) with an experiment and
spectrum name so that it may be visualised and accessed within the current
CCPN project. Spectra of many different origins and file formats may be
loaded, which currently includes Bruker, Varian, Felix, NMRPipe, NmrView,
SPARKY/UCSF, Azara and the factorised shape format "USF3". Depending upon the
file format of the spectrum, data loaded the user may be required to either
select a parameter file which then refers to the actual spectrum intensity
data; this is true for Bruker "procs" and AZARA ".par" files, or alternatively
a spectrum data file itself that contains referencing information; this is
the case for SPARKY/UCSF, NmrView and NMRPipe spectra.
The layout of the popup involved two sections; the upper of which is for
navigating to and selecting the spectrum or parameter files within the
file-system, and the lower is for specifying how each spectrum is loaded into
the CCPN project. It should be noted that when spectrum parameters are read
the first time, the relevant information is copied into the CCPN project,
where it may be adjusted independently of the original file information. No
copies of the spectrum intensity data are made, the CCPN project merely refers
to the spectrum data on disk, although the data file for a loaded spectrum may
subsequently be moved or replaced.
In normal operation the user first selects the kind of spectrum file format
that will be loaded via the upper "File format" pulldown menu and then checks
that the "File type" pulldown (toward the bottom of the file browser) is set
to detect the appropriate kinds of filename; if a helpful file name filter is
not available the user can add one via the "Manual Select" field, taking care
to add any wild-card symbols, like the asterisk in "\*.ft3". Next the spectrum
data or parameter files, appropriate to the selected format, are located by
navigating within the file-system browser. When the required spectrum files are
visible the user selects one *or more* to load. Multiple file selections may
be made using left-click with <Ctrl> (toggle selection) or <Shift> (select
range). It should be noted that when selecting Bruker files, when using the
standard Bruker directory structure, the user only needs to navigate to the
numbered spectrum directory; by default the "procs" file two levels down is
searched for, e.g. "123/pdata/1/procs" is shown in the directory containing
the "123" directory.
When spectrum or parameter files are selected in the file table, the lower
"Spectra To Open" table is filled to reflect the selection. The user should
then be mindful of the settings within this table and may choose to edit
various things by double-clicking on the appropriate cell. Typically the user
just adjusts the name of the independent "Experiment" and "Spectrum" records.
These names are usually concatenated like "expName:specName" in CCPN graphical
displays so there is no need to repeat a name in both fields; this only takes
up more space. The Experiment, which is a record of *what was done
experimentally*, commonly has a short name like "HNCA" or "HSQC_298K" so the
user readily knows how to interpret the experimental data. The Spectrum, which
is a record of *the data that was collected*, commonly has a short name to
identify the spectrum number or file name. An Experiment record may contain
several Spectrum records, so the spectrum's name need minimally only identify
it amongst others from the same experiment. The Shift List value may be
changed if the user knows that the experiment represents a distinct set of
conditions, with different spectrum peak/resonance positions, to existing or
other experiments being entered. Each shift list will be curated separately,
to give separate chemical shift values for assignments made under different
conditions (even when relating to the same atoms). The shift list that an
experiment uses may also be changed at any time after loading.
When all spectra and options are specified the [Open Spectrum] button will
load the relevant data into the CCPN project. If the "Skip verification
dialogs" option is set it is assumed that all of the spectrum point to
frequency referencing information, and any data file references, are correct.
Otherwise, the user will be prompted to confirm the file details and
referencing information for each spectrum in turn. Finally, after loading the
user is asked to set the type of NMR experiment, in terms of general
magnetisation transfer pathway, that was performed.
**Caveats & Tips**
If the name of an Experiment that is *already within the CCPN project* is
used, then the loaded spectrum will (assuming it is compatible) be entered
under that existing experiment record; no new experiment entity will be
defined. The user may legitimately use this feature to load several spectra
that relate to the same experiment; typically where spectra are different
projections. To facilitate this the "Use shared experiment" option can be
selected.
Although experiments and spectra may be renamed after loading, a spectrum
record may not be placed under a different experiment once created; deletion
and re-loading is the only mans of achieving this, and care must be taken in
transferring any assignments.
"""
def __init__(self, parent, *args, **kw):
self.experiment = None
self.currentObject = None
#self.currentObjects = [] # looks obsolete
BasePopup.__init__(self,
parent=parent,
title='Experiment : Open Spectra',
**kw)
def open(self):
self.message()
BasePopup.open(self)
def body(self, guiFrame):
self.fileSelect = None
names, objects = self.getShiftLists()
self.shiftListPulldown = PulldownList(self,
callback=self.setShiftList,
texts=names,
objects=objects)
self.windowPulldown = PulldownList(self,
texts=WINDOW_OPTS,
callback=self.setWindow)
self.experimentEntry = Entry(self,
width=16,
returnCallback=self.setExperiment)
self.spectrumEntry = Entry(self,
width=16,
returnCallback=self.setSpectrum)
guiFrame.grid_columnconfigure(0, weight=1)
guiFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_rowconfigure(1, weight=1)
leftFrame = LabelFrame(guiFrame, text='File Selection')
leftFrame.grid(row=0, column=0, sticky='nsew')
leftFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(leftFrame, text='File format:')
label.grid(row=row, column=0, sticky='w')
tipText = 'Selects which kind of spectrum file is being loaded; what its data matrix format is'
self.formatPulldown = PulldownList(leftFrame,
callback=self.chooseFormat,
texts=file_formats,
tipText=tipText,
grid=(row, 1))
self.detailsLabel = Label(leftFrame, text='Show details:')
tipText = 'Whether to show an annotation that describes the spectrum in the file selection; currently only uses comment fields from Bruker spectra'
self.detailsSelect = CheckButton(leftFrame,
selected=False,
callback=self.showDetails,
tipText=tipText)
self.titleRow = row
self.detailsSelected = False
row = row + 1
leftFrame.grid_rowconfigure(row, weight=1)
file_types = [FileType('All', ['*'])]
self.fileSelect = FileSelect(leftFrame,
multiSelect=True,
file_types=file_types,
single_callback=self.chooseFiles,
extraHeadings=('Details', ),
extraJustifies=('left', ),
displayExtra=False,
getExtraCell=self.getDetails,
manualFileFilter=True)
self.fileSelect.grid(row=row, column=0, columnspan=6, sticky='nsew')
rightFrame = LabelFrame(guiFrame, text='Spectra To Open')
rightFrame.grid(row=1, column=0, sticky='nsew')
rightFrame.grid_columnconfigure(3, weight=1)
row = 0
label = Label(rightFrame,
text='Skip verification dialogs:',
grid=(row, 0))
tipText = 'Whether to allow the user to check file interpretation and referencing information before the spectrum is loaded'
self.verifySelect = CheckButton(rightFrame,
selected=False,
grid=(row, 1),
tipText=tipText)
label = Label(rightFrame, text='Use shared experiment:', grid=(row, 2))
tipText = 'When selecting multiple spectrum files, whether the loaded spectra will all belong to (derive from) the same experiment; useful for projection spectra etc.'
self.sharedExpSelect = CheckButton(rightFrame,
selected=False,
tipText=tipText,
callback=self.useShared,
grid=(row, 3))
row = row + 1
rightFrame.grid_rowconfigure(row, weight=1)
tipTexts = [
'A short textual name for the experiment record that the loaded spectrum will belong to; may be a new experiment or the name of an existing one',
'A short textual name to identify the spectrum within its experiment; typically a few characters or spectrum number, rather than a repeat of the experiment name',
'The location of the file, relative to the current directory, that the spectrum data will be loaded from',
'Sets which window or windows the spectrum will initially appear within once loaded',
'Sets which shift list the experiment (and hence loaded spectrum) will use to curate chemical shift information; can be changed after load time'
]
headingList = [
'Experiment', 'Spectrum', 'File', 'Windows', 'Shift List'
]
editWidgets = [
self.experimentEntry, self.spectrumEntry, None,
self.windowPulldown, self.shiftListPulldown
]
editGetCallbacks = [
self.getExperiment, self.getSpectrum, None, self.getWindow,
self.getShiftList
]
editSetCallbacks = [
self.setExperiment, self.setSpectrum, None, self.setWindow,
self.setShiftList
]
self.scrolledMatrix = ScrolledMatrix(rightFrame,
headingList=headingList,
callback=self.selectCell,
editWidgets=editWidgets,
multiSelect=True,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
tipTexts=tipTexts,
grid=(row, 0),
gridSpan=(1, 4))
row = row + 1
tipTexts = [
'Load spectrum or spectra into the CCPN project using the selected file(s)',
]
texts = ['Open Spectrum']
commands = [self.openSpectra]
bottomButtons = UtilityButtonList(guiFrame,
texts=texts,
tipTexts=tipTexts,
doClone=False,
commands=commands,
helpUrl=self.help_url)
bottomButtons.grid(row=row, column=0, columnspan=1, sticky='ew')
self.openButton = bottomButtons.buttons[0]
self.chooseFormat('Azara')
self.message()
def message(self):
if not self.project or len(self.nmrProject.experiments) < 1:
pass
#self.parent.ticker.setMessage('Choose spectrum files to open.... ')
def showDetails(self, isSelected):
self.detailsSelected = isSelected
self.fileSelect.updateDisplayExtra(isSelected)
# below is so that when Details column is toggled on it will actually
# be seen without having to use the scrollbar
self.fileSelect.fileList.refreshSize()
def useShared(self, isSelected):
self.chooseFiles(forceUpdate=True)
#if isSelected:
#objects = self.scrolledMatrix.objectList
#if len(objects) > 1:
# self.currentObject = objects[0]
# text = objects[0][0]
# self.chooseFiles()
# for oo in objects[1:]:
# oo[0] = text
# if self.project:
# self.experiment = self.nmrProject.findFirstExperiment(name=text)
#self.update()
def gridDetails(self, bool):
if bool:
self.detailsLabel.grid(row=self.titleRow, column=2, sticky='w')
self.detailsSelect.grid(row=self.titleRow, column=3, sticky='w')
self.fileSelect.updateDisplayExtra(self.detailsSelected)
else:
self.detailsLabel.grid_forget()
self.detailsSelect.grid_forget()
self.fileSelect.updateDisplayExtra(False)
def openSpectra(self):
noVerify = self.verifySelect.getSelected()
# tracks if 'add to existing experiment' has already ben OK'ed
self.okExpSet = set()
directory = self.fileSelect.getDirectory()
spectra = []
specIndex = 0
for obj in self.scrolledMatrix.objectList:
fileName = uniIo.joinPath(directory, obj.fileName)
spectrum = self.openSpectrum(obj.exptName, obj.specName, fileName,
obj.window, obj.shiftListName)
specIndex += 1
if (spectrum):
# check endianness if we are not verifying
spectra.append(spectrum)
if noVerify:
isBigEndian = isSpectrumBigEndian(
spectrum) # according to data in file
if isBigEndian is not None:
isBigEndianCurr = getIsSpectrumBigEndian(
spectrum) # according to data model
setIsSpectrumBigEndian(spectrum, isBigEndian)
if isBigEndian != isBigEndianCurr:
if isBigEndian:
s = 'big'
else:
s = 'little'
print 'WARNING: swapped endianess of spectrum to %s endian' % s
#
del self.okExpSet
if noVerify and len(spectra) > 1 and self.sharedExpSelect.getSelected(
):
# if we are using a shared experiment and not verifying,
# set referencing to match first spectrum for all
# get reference spectrum and set up data structure
# use most recent pre-existing spectrum, otherwise first new one
refSpec = spectra[0]
for spec in spectra[0].experiment.sortedDataSources():
if spec in spectra:
break
else:
refSpec = spec
ddrLists = {}
refDdrs = []
for dataDim in refSpec.sortedDataDims():
for ddr in dataDim.dataDimRefs:
ddrLists[ddr.expDimRef] = []
refDdrs.append(ddr)
# get dataDimRefs, store by ExpDimRef,
# checking that all spectra have data dim refs for same set of xdr
nTotal = len(ddrLists)
for spec in spectra:
nFound = 0
for dataDim in spec.sortedDataDims():
for ddr in dataDim.dataDimRefs:
xdr = ddr.expDimRef
ll = ddrLists.get(xdr)
if ll is None:
# something did not match - do nothing
break
else:
ll.append(ddr)
nFound += 1
else:
if nFound == nTotal:
# we are OK. Do next spectrum
continue
# something did not match - do nothing
break
else:
# all spectra matched. Now reset O1 references to match reference
if refSpec is spectra[0]:
startAt = 1
else:
startAt = 0
for refDdr in refDdrs:
dataDim = refDdr.dataDim
centrePoint = dataDim.numPointsOrig / 2 - dataDim.pointOffset + 1
refValue = refDdr.pointToValue(centrePoint)
xdr = refDdr.expDimRef
for ddr in ddrLists[xdr][startAt:]:
dataDim = ddr.dataDim
centrePoint = dataDim.numPointsOrig / 2 - dataDim.pointOffset + 1
ddr.refPoint = centrePoint
ddr.refValue = refValue
# set refExperiment if there is only one possibility
experiments = []
ignoreSet = set()
showPopup = False
for spectrum in spectra:
experiment = spectrum.experiment
if experiment not in ignoreSet:
ignoreSet.add(experiment)
if not experiment.refExperiment:
experiments.append(spectrum.experiment)
if noVerify:
resetCategory = False
if not hasattr(experiment, 'category'):
if (hasattr(experiment, 'pulProgName')
and hasattr(experiment, 'pulProgType')):
# this is first time we get here, and we have external name and source
# use external source to set fullType
experiment.category = 'use external'
resetCategory = True
refExperiments = getRefExperiments(experiment)
if resetCategory and not refExperiments:
# no refExperiments match external source.
# unset 'use external' category
del experiment.category
if len(refExperiments) == 1:
# only one possibility, just set it
setRefExperiment(experiment, refExperiments[0])
# wb104: 20 Oct 2014: do not popup Experiment types dialog if noVerify
#else:
# showPopup = True
# Pop up refExperiment verification
if experiments and (showPopup or not noVerify):
self.parent.initRefExperiments(experiments)
# set up internal Analysis data
for spectrum in spectra:
self.parent.finishInitSpectrum(spectrum)
print 'finished opening spectrum', spectrum.experiment.name, spectrum.name
def chooseFiles(self, forceUpdate=False, *file):
directory = self.fileSelect.getDirectory()
fileNames = self.fileSelect.fileList.currentObjects
fullFileNames1 = [uniIo.joinPath(directory, x) for x in fileNames]
fullFileNames2 = [x.fileName for x in self.scrolledMatrix.objectList]
fullFileNames2 = [uniIo.joinPath(directory, x) for x in fullFileNames2]
if fullFileNames1 == fullFileNames2 and not forceUpdate:
return
objectList = []
textMatrix = []
format = self.formatPulldown.getText()
shiftListName = self.getShiftLists()[0][0]
windowOpt = WINDOW_OPTS[1]
oneUp = os.path.dirname
if format == 'Bruker':
if self.sharedExpSelect.getSelected():
nameTemplate = 'Bruker_%d'
next = self.getNextExpNum(nfiles=len(fileNames),
nameTemplate=nameTemplate)
exptName = nameTemplate % (next)
for i, fileName in enumerate(fileNames):
fullFileName = fullFileNames1[i]
specName = os.path.basename(
oneUp(oneUp(oneUp(fullFileName))))
datum = (exptName, specName, fileName, windowOpt,
shiftListName)
dataObj = RowObject(*datum)
textMatrix.append(datum)
objectList.append(dataObj)
else:
for i, fileName in enumerate(fileNames):
fullFileName = fullFileNames1[i]
try: # below should not fail
ss1 = oneUp(fullFileName)
specName = os.path.basename(ss1)
ss2 = os.path.basename(oneUp(oneUp(ss1)))
exptName = 'Bruker_' + ss2
except: # just put in something
ss = os.path.basename(fullFileName)
exptName = 'Bruker_' + ss
specName = ss
datum = (exptName, specName, fileName, windowOpt,
shiftListName)
dataObj = RowObject(*datum)
textMatrix.append(datum)
objectList.append(dataObj)
else:
next = self.getNextExpNum(nfiles=len(fileNames))
if self.sharedExpSelect.getSelected():
exptName = 'Expt_%d' % (next)
for i, fileName in enumerate(fileNames):
specName = re.sub('\.\w+$', '', fileName)
datum = (exptName, specName, fileName, windowOpt,
shiftListName)
dataObj = RowObject(*datum)
textMatrix.append(datum)
objectList.append(dataObj)
else:
for i, fileName in enumerate(fileNames):
exptName = 'Expt_%d' % (next + i)
specName = re.sub('\.\w+$', '', fileName)
datum = (exptName, specName, fileName, windowOpt,
shiftListName)
dataObj = RowObject(*datum)
textMatrix.append(datum)
objectList.append(dataObj)
if len(fileNames) > 1:
self.openButton.config(text='Open Spectra')
else:
self.openButton.config(text='Open Spectrum')
self.scrolledMatrix.update(objectList=objectList,
textMatrix=textMatrix)
def getNextExpNum(self, nfiles=0, nameTemplate='Expt_%d'):
""" get suitable free integer to use for exp names
"""
next = 1
if self.project:
nmrProject = self.nmrProject
ii = len(nmrProject.experiments)
# find first exp number that is not taken
# NBNB TBD could consider expname = specname, specname = proc dir
next = ii + 1
if nfiles:
while ii < next + nfiles:
ii += 1
if nmrProject.findFirstExperiment(name=nameTemplate % ii):
next = ii + 1
#
return next
def getDetails(self, fullfile):
details = ''
if os.path.isfile(fullfile):
format = self.formatPulldown.getText()
detailsDir = os.path.dirname(fullfile)
detailsFile = uniIo.joinPath(detailsDir, details_file_dict[format])
if os.path.exists(detailsFile):
fp = open(detailsFile)
details = fp.read().strip().replace('\n',
' ').replace('\r', ' ')
fp.close()
return (details, )
def update(self):
objectList = self.scrolledMatrix.objectList
textMatrix = [(obj.exptName, obj.specName, obj.fileName, obj.window,
obj.shiftListName) for obj in objectList]
self.scrolledMatrix.update(objectList=objectList,
textMatrix=textMatrix)
def selectCell(self, obj, row, col):
self.currentObject = obj
if self.project:
self.experiment = self.nmrProject.findFirstExperiment(
name=obj.exptName)
else:
self.experiment = None
def getWindow(self, obj):
if obj:
self.windowPulldown.set(obj.window)
def setWindow(self, opt):
if isinstance(opt, RowObject):
self.currentObject.window = opt.window
else:
self.currentObject.window = opt
self.update()
def setShiftList(self, obj=None):
if self.project:
project = self.project
shiftList = self.shiftListPulldown.getObject()
if shiftList is None:
shiftList = newShiftList(project, unit='ppm')
if self.experiment and shiftList and (
shiftList is not self.experiment.shiftList):
setExperimentShiftList(self.experiment, shiftList)
self.currentObject.shiftListName = shiftList.name
self.update()
def getShiftList(self, object):
names, shiftLists = self.getShiftLists()
if names:
self.shiftListPulldown.setup(names, shiftLists, 0)
if self.experiment and self.experiment.shiftList:
name = self.experiment.shiftList.name
else:
name = object.shiftListName
if name is not None:
self.shiftListPulldown.set(name)
def getShiftLists(self):
if self.project:
names = []
objects = getShiftLists(self.nmrProject)
for shiftList in objects:
if not shiftList.name:
shiftList.name = 'ShiftList %d' % shiftList.serial
names.append(shiftList.name)
objects.append(None)
names.append('<New>')
else:
objects = [
None,
]
names = [
'ShiftList 1',
]
return names, objects
def chooseFormat(self, format):
if format in ('Bruker', 'Varian'):
self.gridDetails(True)
else:
self.gridDetails(False)
file_types = []
file_type = file_type_dict.get(format)
if (file_type):
file_types.extend([file_type])
file_types.append(FileType('All', ['*']))
file_types.append(self.fileSelect.manualFilter)
self.fileSelect.setFileTypes(file_types)
def getSpectrum(self, obj):
if obj:
self.spectrumEntry.set(obj.specName)
def setSpectrum(self, *event):
if self.currentObject:
text = self.spectrumEntry.get()
if text and text != ' ':
for data in self.scrolledMatrix.objectList:
if data is self.currentObject:
continue
if (data.specName
== text) and (data.exptName
== self.currentObject.exptName):
showWarning(
'Repeated name',
'Spectrum name (%s) already in use for experiment (%s)'
% (data.specName, data.exptName),
parent=self)
return
elif (self.experiment) and (
self.experiment.findFirstDataSource(name=text)):
showWarning(
'Repeated name',
'Spectrum name (%s) already in use for experiment (%s)'
% (data.specName, data.exptName),
parent=self)
return
self.currentObject.specName = text
self.update()
def getExperiment(self, obj):
if obj:
self.experimentEntry.set(obj.exptName)
def setExperiment(self, *event):
if self.currentObject:
text = self.experimentEntry.get()
if text and text != ' ':
if self.sharedExpSelect.getSelected():
# share one experiment for all rows
for oo in self.scrolledMatrix.objectList:
oo.exptName = text
else:
#separate experiments
self.currentObject.exptName = text
if self.project:
self.experiment = self.nmrProject.findFirstExperiment(
name=text)
self.update()
def updateShiftLists(self):
if self.project:
name = self.expt_entry.get()
e = self.nmrProject.findFirstExperiment(name=name)
else:
e = None
names, objects = self.getShiftLists()
if e and e.shiftList:
index = objects.index(e.shiftList)
else:
index = 0
self.shiftListPulldown.setup(names, objects, index)
def openSpectrum(self,
exptName,
specName,
file,
windowOpt=WINDOW_OPTS[2],
shiftListName='<New>',
extraData=None):
# input checks
if not file:
showError('No file', 'Need to enter file', parent=self)
return None
if not exptName:
showError('Experiment',
'Need to enter experiment name',
parent=self)
return None
if not specName:
showError('Spectrum', 'Need to enter spectrum name', parent=self)
return None
# get or set up project
project = self.project
if not project:
self.project = project = defaultProject()
self.parent.initProject(project)
self.nmrProject = self.parent.nmrProject
self.analysisProject = self.parent.analysisProject
#Default ShiftList with name 'ShiftList 1' created
# set up shift list
if shiftListName == '<New>':
shiftList = None
else:
shiftList = self.nmrProject.findFirstMeasurementList(
className='ShiftList', name=shiftListName)
# read params
format = self.formatPulldown.getText()
clazz = params_class_dict[format]
try:
params = clazz(file, extraData=extraData)
except Implementation.ApiError, e:
showError('Reading params file',
'Fatal error: ' + e.error_msg,
parent=self)
return None
dim = params.pseudoDataDim()
if dim is not None:
if format == 'NMRPipe':
popup = NmrPipePseudoPopup(self, params, dim, file)
popup.destroy()
elif format == 'Bruker':
popup = BrukerPseudoPopup(self, params, dim)
popup.destroy()
# get or set up experiment
experiment = self.nmrProject.findFirstExperiment(name=exptName)
if experiment:
expIsNew = False
if experiment.findFirstDataSource(name=specName):
showError('Duplicate name',
'Duplicate spectrum name "%s" in experiment %s' %
(specName, experiment.name),
parent=self)
return None
elif (experiment.dataSources and experiment not in self.okExpSet):
if showOkCancel('Multiple Spectra Warning',
'Really put multiple '
'spectra into existing experiment %s?' %
experiment.name,
parent=self):
self.okExpSet.add(experiment)
else:
return
else:
expIsNew = True
try:
# Will also work for shiftList == None
experiment = Nmr.Experiment(self.nmrProject,
name=exptName,
numDim=params.ndim,
shiftList=shiftList)
except Implementation.ApiError, experiment:
showError('Experiment', experiment.error_msg, parent=self)
return None