def addAuiTab(self, tabName, evidenceDetails):
global caseDir
for x in caseDetails:
caseDir = x[4]
if tabName == "Summary":
self.auiNotebook.AddPage(
SummaryTab.TabPanel(self.auiNotebook, caseDetails,
evidenceDetails), tabName, False,
wx.NullBitmap)
if tabName == "File":
self._dialog = wx.ProgressDialog(
"Loading", "Loading {tabName}".format(tabName=tabName),
100) #create loading dialog
LoadingDialog(self._dialog) #start loading
self.auiNotebook.AddPage(
pcapFilesTab.FilesTabPanel(self.auiNotebook, tabName,
caseDir), tabName, False, wx.
NullBitmap) #calls and open a aui tab from DeletedFilesTab.py
LoadingDialog.endLoadingDialog(self)
if tabName == "Images":
self._dialog = wx.ProgressDialog(
"Loading", "Loading {tabName}".format(tabName=tabName),
100) #create loading dialog
LoadingDialog(self._dialog) #start loading
self.auiNotebook.AddPage(
ImagesTab.TabPanel(self.auiNotebook, tabName,
caseDir), tabName, False, wx.NullBitmap
) #calls and open a aui tab from DeletedFilesTab.py
LoadingDialog.endLoadingDialog(self)
if tabName == "Sessions":
self._dialog = wx.ProgressDialog(
"Loading", "Loading {tabName}".format(tabName=tabName),
100) #create loading dialog
LoadingDialog(self._dialog) #start loading
self.auiNotebook.AddPage(
pcapSessionsTab.SessionsTabPanel(self.auiNotebook,
caseDir), tabName, False, wx.
NullBitmap) #calls and open a aui tab from DeletedFilesTab.py
LoadingDialog.endLoadingDialog(self)
if tabName == "DNS":
self._dialog = wx.ProgressDialog(
"Loading", "Loading {tabName}".format(tabName=tabName),
100) #create loading dialog
LoadingDialog(self._dialog) #start loading
self.auiNotebook.AddPage(
pcapDNSTab.DNSTabPanel(self.auiNotebook,
caseDir), tabName, False, wx.NullBitmap
) #calls and open a aui tab from DeletedFilesTab.py
LoadingDialog.endLoadingDialog(self)
if tabName == "Credentials":
self._dialog = wx.ProgressDialog(
"Loading", "Loading {tabName}".format(tabName=tabName),
100) #create loading dialog
LoadingDialog(self._dialog) #start loading
self.auiNotebook.AddPage(
pcapCredentialsTab.CredTabPanel(self.auiNotebook, tabName,
caseDir), tabName, False, wx.
NullBitmap) #calls and open a aui tab from DeletedFilesTab.py
LoadingDialog.endLoadingDialog(self)
if tabName == "Bookmarks":
self._dialog = wx.ProgressDialog(
"Loading", "Loading {tabName}".format(tabName=tabName), 100)
LoadingDialog(self._dialog)
self.auiNotebook.AddPage(
AnalyzedDataTab.TabPanel(self.auiNotebook, tabName,
evidenceDetails, caseDir, caseDbPath),
tabName, False,
wx.NullBitmap) #calls and open a aui tab from SummaryTab.py
LoadingDialog.endLoadingDialog(self)
# TODO un-comment-out the following code once evidence exists properly
# note: commented-out to allow File tab to be tested before database code added
"""for x in evidenceDetails:
def takeProjectedSlice(self, axes, projectionAxis, shouldTransform,
order = 1):
if (projectionAxis == 2 or
(numpy.all(self.alignParams[:,3] == 0) and
numpy.all(self.alignParams[:,4] == 1))):
# Scaling/rotation doesn't affect the projection; lucky us!
data = self.imageArray.max(axis = projectionAxis)
# Augment data with an extra dimension to replace the one we
# flattened out.
data = numpy.expand_dims(data, projectionAxis)
# Since we flattened out this axis, change its index to be the only
# possible valid index.
axes[projectionAxis] = 0
return self.takeSliceFromData(data, axes, shouldTransform, order)
elif projectionAxis in [3, 4]:
# Projecting through Y or X; just transform the local volume.
dialog = wx.ProgressDialog(
title = "Constructing projection",
message = "Please wait...",
maximum = self.size[0],
style = wx.PD_AUTO_HIDE | wx.PD_REMAINING_TIME)
curTimepoint = self.curViewIndex[1]
data = []
for wavelength in range(self.size[0]):
data.append(self.transformArray(
self.imageArray[wavelength, curTimepoint],
*self.alignParams[wavelength],
order = 1))
dialog.Update(wavelength)
data = numpy.array(data, dtype = self.dtype)
dialog.Destroy()
return data.max(axis = projectionAxis - 1)
else:
# Projecting through time; transform EVERY volume. Ouch.
dialog = wx.ProgressDialog(
title = "Constructing projection",
message = "Please wait...",
maximum = self.size[0] * self.size[1],
style = wx.PD_AUTO_HIDE | wx.PD_REMAINING_TIME)
data = []
for timepoint in range(self.size[1]):
timeData = []
for wavelength in range(self.size[0]):
volume = self.transformArray(
self.imageArray[wavelength, timepoint],
*self.alignParams[wavelength],
order = 1)
timeData.append(volume)
dialog.Update(timepoint * self.size[0] + wavelength)
timeData = numpy.array(timeData, dtype = self.dtype)
data.append(timeData)
data = numpy.array(data, dtype = self.dtype)
data = data.max(axis = 0)
dialog.Destroy()
# Slice through data per our axes parameter.
slice = [Ellipsis] * 4
for axis, position in axes.items():
if axis != 1:
slice[axis - 1] = position
return data[slice]
raise RuntimeError("Couldn't find a valid slice axis.")
def onBtnScan(self, evt):
filename = wx.FileSelector("Choose a file to scan")
if filename != "":
config = wx.ConfigBase.Get()
config.SetPath("/Scanning")
use_md5 = config.ReadBool("use_md5_checksums", use_md5_default)
use_sha1 = config.ReadBool("use_sha1_checksums", use_sha1_default)
use_sha256 = config.ReadBool("use_sha256_checksums",
use_sha256_default)
use_chunks = config.ReadBool("use_chunk_checksums",
use_chunks_default)
max_chunks = config.ReadInt("max_chunk_checksums",
max_chunks_default)
size_chunks = config.ReadInt("min_chunk_size", chunk_size_default)
old_filename = self.mlfile.filename
progressdlg = wx.ProgressDialog(
"Scanning file...",
"Please wait while Metalink Editor scans the selected file. This can take some time for very large files.",
100, self, wx.PD_AUTO_HIDE | wx.PD_APP_MODAL | wx.PD_CAN_ABORT
| wx.PD_ELAPSED_TIME | wx.PD_REMAINING_TIME
| wx.PD_ESTIMATED_TIME)
success = self.mlfile.scan_file(filename, use_chunks, max_chunks,
size_chunks, progressdlg)
progressdlg.Destroy()
if not success: return
self.txtctrl_size.SetValue(str(self.mlfile.size))
self.txtctrl_filename.SetValue(self.mlfile.filename)
md5val = ""
if use_md5:
md5val = self.mlfile.hashlist['md5']
self.txtctrl_md5.SetValue(md5val)
sha1val = ""
if use_sha1:
sha1val = self.mlfile.hashlist['sha1']
self.txtctrl_sha1.SetValue(sha1val)
sha256val = ""
if use_sha256:
sha256val = self.mlfile.hashlist['sha256']
self.txtctrl_sha256.SetValue(sha256val)
if self.mlfile.hashlist['sha256'] == "":
self.txtctrl_sha256.Enable(False) # No support for SHA-256
# Update URLs
num_urls = self.filelist.GetItemCount()
new_filename = self.mlfile.filename
if num_urls > 0 and new_filename != old_filename:
answer = wx.MessageBox(
"Would you like to update your URLs, so that they use the new filename instead of the old?",
"Update mirrors?", wx.ICON_QUESTION | wx.YES_NO, self)
if answer == wx.YES:
print "\nUpdating mirrors with the new filename."
print "Changing", old_filename, "to", new_filename + "."
item = -1
while True:
item = self.filelist.GetNextItem(
item, wx.LIST_NEXT_ALL, wx.LIST_STATE_DONTCARE)
if item == -1: break
url = self.filelist.GetItem(item, 0).GetText()
#if old_filename == "":
url = os.path.dirname(url) + "/" + new_filename
self.filelist.SetStringItem(item, 0, url)
#else:
# pos = url.rfind(old_filename)
# if pos != -1:
# print "Updated", url
# url = url[:pos] + new_filename
# self.filelist.SetStringItem(item, 0, url)
item = -1
while True:
item = self.filelist.GetNextItem(item, wx.LIST_NEXT_ALL,
wx.LIST_STATE_DONTCARE)
if item == -1: break
url = self.filelist.GetItem(item, 0).GetText()
if url.startswith("ed2k://"):
# remove ed2k links, they add themselves back in later
self.filelist.DeleteItem(item)
if url.startswith("magnet:"):
# remove magnet links, they add themselves back in later
self.filelist.DeleteItem(item)
# add ed2k and magnet link to GUI for this file
if self.mlfile.ed2k != "":
self.addurl(metalink.Resource(self.mlfile.ed2k))
if self.mlfile.magnet != "":
self.addurl(metalink.Resource(self.mlfile.magnet))
self.filename = filename + ".metalink"
self.new_file = True
self.locked = True
self.update()
def Run(self):
# load board
board = pcbnew.GetBoard()
# go to the project folder - so that log will be in proper place
os.chdir(os.path.dirname(os.path.abspath(board.GetFileName())))
# Remove all handlers associated with the root logger object.
for handler in logging.root.handlers[:]:
logging.root.removeHandler(handler)
# set up logger
logging.basicConfig(
level=logging.DEBUG,
filename="replicate_layout.log",
filemode='w',
format='%(asctime)s %(name)s %(lineno)d:%(message)s',
datefmt='%m-%d %H:%M:%S')
logger = logging.getLogger(__name__)
logger.info("Replicate layout plugin version: " + VERSION + " started")
stdout_logger = logging.getLogger('STDOUT')
sl_out = StreamToLogger(stdout_logger, logging.INFO)
sys.stdout = sl_out
stderr_logger = logging.getLogger('STDERR')
sl_err = StreamToLogger(stderr_logger, logging.ERROR)
sys.stderr = sl_err
_pcbnew_frame = [
x for x in wx.GetTopLevelWindows()
if x.GetTitle().lower().startswith('pcbnew')
][0]
# check if there is exactly one module selected
selected_modules = [
x for x in pcbnew.GetBoard().GetModules() if x.IsSelected()
]
selected_names = []
for mod in selected_modules:
selected_names.append("{}".format(mod.GetReference()))
# if more or less than one show only a messagebox
if len(selected_names) != 1:
caption = 'Replicate Layout'
message = "More or less than 1 footprints selected. Please select exactly one footprint and run the script again"
dlg = wx.MessageDialog(_pcbnew_frame, message, caption,
wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
dlg.Destroy()
logging.shutdown()
return
# if exactly one module is selected
# this is a pivot module
pivot_module_reference = selected_names[0]
# prepare the replicator
logger.info("Preparing replicator with " + pivot_module_reference +
" as a reference")
try:
replicator = replicatelayout.Replicator(board,
self.update_progress)
except LookupError as exception:
caption = 'Replicate Layout'
message = str(exception)
dlg = wx.MessageDialog(_pcbnew_frame, message, caption,
wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
dlg.Destroy()
logging.shutdown()
return
except Exception:
logger.exception(
"Fatal error when making an instance of replicator")
caption = 'Replicate Layout'
message = "Fatal error when making an instance of replicator.\n"\
+ "You can raise an issue on GiHub page.\n" \
+ "Please attach the replicate_layout.log which you should find in the project folder."
dlg = wx.MessageDialog(_pcbnew_frame, message, caption,
wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
dlg.Destroy()
logging.shutdown()
return
pivot_mod = replicator.get_mod_by_ref(pivot_module_reference)
logger.info("Pivot footprint is %s\nLocated on:%s\nWith filenames:%s\nWith sheet_id:%s" \
% (repr(pivot_mod.ref), repr(pivot_mod.sheet_id), repr(pivot_mod.filename), repr(pivot_mod.sheet_id)))
list_of_modules_with_same_id = replicator.get_list_of_modules_with_same_id(
pivot_mod.mod_id)
nice_list = [(x.ref, x.sheet_id) for x in list_of_modules_with_same_id]
logger.info("Corresponding footprints are \n%s" % repr(nice_list))
list_of_modules = replicator.get_list_of_modules_with_same_id(
pivot_mod.mod_id)
if not list_of_modules:
caption = 'Replicate Layout'
message = "Selected footprint is uniqe in the pcb (only one footprint with this ID)"
dlg = wx.MessageDialog(_pcbnew_frame, message, caption,
wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
dlg.Destroy()
logging.shutdown()
return
# show dialog
logger.info("Showing dialog")
dlg = ReplicateLayoutDialog(_pcbnew_frame, replicator,
pivot_module_reference)
res = dlg.ShowModal()
# clear highlight on all modules on selected level
for mod in dlg.pivot_modules:
clear_highlight_on_module(mod)
pcbnew.Refresh()
if res == wx.ID_OK:
selected_items = dlg.list_sheets.GetSelections()
slected_names = []
for sel in selected_items:
slected_names.append(dlg.list_sheets.GetString(sel))
replicate_containing_only = not dlg.chkbox_intersecting.GetValue()
remove_existing_nets_zones = dlg.chkbox_remove.GetValue()
rep_tracks = dlg.chkbox_tracks.GetValue()
rep_zones = dlg.chkbox_zones.GetValue()
rep_text = dlg.chkbox_text.GetValue()
rep_drawings = dlg.chkbox_drawings.GetValue()
else:
logger.info("User canceled the dialog")
logging.shutdown()
return
# failsafe somtimes on my machine wx does not generate a listbox event
level = dlg.list_levels.GetSelection()
selection_indeces = dlg.list_sheets.GetSelections()
sheets_on_a_level = replicator.get_sheets_to_replicate(
pivot_mod, pivot_mod.sheet_id[level])
sheets_for_replication = [
sheets_on_a_level[i] for i in selection_indeces
]
# check if all the anchor footprints are on the same layer as pivot footprint
# first get all the anchor footprints
all_sheet_footprints = []
for sheet in sheets_for_replication:
all_sheet_footprints.extend(replicator.get_modules_on_sheet(sheet))
anchor_fp = [
x for x in all_sheet_footprints if x.mod_id == pivot_mod.mod_id
]
# then check if all of them are on the same layer
if not all(fp.mod.IsFlipped() == pivot_mod.mod.IsFlipped()
for fp in anchor_fp):
caption = 'Replicate Layout'
message = "Anchor footprints must be on the same layer as pivot footprint!"
dlg = wx.MessageDialog(_pcbnew_frame, message, caption,
wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
dlg.Destroy()
logging.shutdown()
return
# replicate now
logger.info("Replicating layout")
self.start_time = time.time()
self.last_time = self.start_time
self.dlg = wx.ProgressDialog("Preparing for replication",
"Starting plugin",
maximum=100)
self.dlg.Show()
self.dlg.ToggleWindowStyle(wx.STAY_ON_TOP)
try:
replicator.replicate_layout(pivot_mod,
pivot_mod.sheet_id[0:level + 1],
sheets_for_replication,
containing=replicate_containing_only,
remove=remove_existing_nets_zones,
tracks=rep_tracks,
zones=rep_zones,
text=rep_text,
drawings=rep_drawings)
logger.info("Replication complete")
pcbnew.Refresh()
logging.shutdown()
self.dlg.Destroy()
except LookupError as exception:
caption = 'Replicate Layout'
message = str(exception)
dlg = wx.MessageDialog(_pcbnew_frame, message, caption,
wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
dlg.Destroy()
logging.shutdown()
self.dlg.Destroy()
return
except Exception:
logger.exception("Fatal error when running replicator")
caption = 'Replicate Layout'
message = "Fatal error when running replicator.\n"\
+ "You can raise an issue on GiHub page.\n" \
+ "Please attach the replicate_layout.log which you should find in the project folder."
dlg = wx.MessageDialog(_pcbnew_frame, message, caption,
wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
dlg.Destroy()
logging.shutdown()
self.dlg.Destroy()
return
#Reduce verbosity
experiment.exp.verbose = False
experiment.exp.inst.verbose = False
# create initial population
pop = DetectorChoicePopulation()
#Steps in calculation
max = 100
if gui:
import wx
prog_dlg = wx.ProgressDialog(
"Optimizing detector choice using Genetic Algorithm",
"Starting...\n\n\n",
max,
style=wx.PD_CAN_ABORT | wx.PD_APP_MODAL | wx.PD_AUTO_HIDE,
)
prog_dlg.SetSize(wx.Size(500, 200))
prog_dlg.Update(0)
latest_avg = []
num_to_quit = 20
keep_going = True
skipit = False
count = 0
while keep_going:
thebest = pop.best().fitness()
theavg = pop.fitness()
def addAuiTab(self, tabName, evidenceDetails):
global caseDir
for x in caseDetails:
caseDir = x[4]
if tabName == "Summary":
self.auiNotebook.AddPage(
SummaryTab.TabPanel(self.auiNotebook, caseDetails,
evidenceDetails), tabName, False,
wx.NullBitmap)
if tabName == "Deleted files":
self._dialog = wx.ProgressDialog(
"Loading", "Loading {tabName}".format(tabName=tabName),
100) #create loading dialog
LoadingDialog(self._dialog) #start loading
self.auiNotebook.AddPage(
DeletedFilesTab.TabPanel(self.auiNotebook, tabName,
caseDir), tabName, False, wx.
NullBitmap) #calls and open a aui tab from DeletedFilesTab.py
LoadingDialog.endLoadingDialog(self) #stop loading
if tabName == "Bookmarks":
self._dialog = wx.ProgressDialog(
"Loading", "Loading {tabName}".format(tabName=tabName), 100)
LoadingDialog(self._dialog)
self.auiNotebook.AddPage(
AnalyzedDataTab.TabPanel(self.auiNotebook, tabName,
evidenceDetails, caseDir, caseDbPath),
tabName, False,
wx.NullBitmap) #calls and open a aui tab from SummaryTab.py
LoadingDialog.endLoadingDialog(self)
for x in analyzedDataTree:
if tabName == x and tabName != "Deleted files":
self._dialog = wx.ProgressDialog(
"Loading", "Loading {tabName}".format(tabName=tabName),
100)
LoadingDialog(self._dialog)
addingPage = self.auiNotebook.AddPage(
AnalyzedDataTab.TabPanel(self.auiNotebook, tabName,
evidenceDetails, caseDir,
caseDbPath), tabName, False,
wx.NullBitmap)
LoadingDialog.endLoadingDialog(self)
for x in documentsTree:
if tabName == x:
self._dialog = wx.ProgressDialog(
"Loading", "Loading {tabName}".format(tabName=tabName),
100)
LoadingDialog(self._dialog)
self.auiNotebook.AddPage(
AnalyzedDataTab.TabPanel(self.auiNotebook, tabName,
evidenceDetails, caseDir,
caseDbPath), tabName, False,
wx.NullBitmap)
LoadingDialog.endLoadingDialog(self)
for x in executablesTree:
if tabName == x:
self._dialog = wx.ProgressDialog(
"Loading", "Loading {tabName}".format(tabName=tabName),
100)
LoadingDialog(self._dialog)
self.auiNotebook.AddPage(
AnalyzedDataTab.TabPanel(self.auiNotebook, tabName,
evidenceDetails, caseDir,
caseDbPath), tabName, False,
wx.NullBitmap)
LoadingDialog.endLoadingDialog(self)
for x in evidenceDetails:
evidenceDbConn = connectdb.create_connection(
x[2]) #connects to tsk database
evidenceDbInfo = connectdb.select_image_info(
evidenceDbConn) #get name, size and md5 from tsk database
evidencePart = connectdb.select_image_partitions(
evidenceDbConn) #get partition info from tsk database
count = 0
for i in evidencePart:
count += 1
if tabName == "Vol{count} {desc}: {start}-{end})".format(
count=count,
desc=str(i[2]),
start=str(i[0]),
end=str(i[1])):
self._dialog = wx.ProgressDialog(
"Loading", "Loading {tabName}".format(tabName=tabName),
100)
LoadingDialog(self._dialog)
self.auiNotebook.AddPage(
AnalyzedDataTab.TabPanel(self.auiNotebook, tabName,
evidenceDetails, caseDir,
caseDbPath), tabName, False,
wx.NullBitmap)
LoadingDialog.endLoadingDialog(self)
def Export(self):
# use the LONGEST title here! That determines the size of the Dialog Box.
progress = wx.ProgressDialog(_('Transana Selective Data Export'), _('Exporting Transcript records (This may be slow because of the size of Transcript records.)'), style = wx.PD_APP_MODAL | wx.PD_AUTO_HIDE)
if progress.GetSize()[0] > 800:
progress.SetSize((800, progress.GetSize()[1]))
progress.Centre()
db = DBInterface.get_db()
try:
# Get the user specified file name
fs = self.XMLFile.GetValue()
# Ensure that the file name has the proper extension
if (fs[-4:].lower() != '.xml') and (fs[-4:].lower() != '.tra'):
fs = fs + '.tra'
# On the Mac, if no path is specified, the data is exported to a file INSIDE the application bundle,
# where no one will be able to find it. Let's put it in the user's HOME directory instead.
# I'm okay with not handling this on Windows, where it will be placed in the Program's folder
# but it CAN be found. (There's no easy way on Windows to determine the location of "My Documents"
# especially if the user has moved it.)
if "__WXMAC__" in wx.PlatformInfo:
# if the specified file has no path specification ...
if fs.find(os.sep) == -1:
# ... then prepend the HOME folder
fs = os.getenv("HOME") + os.sep + fs
# Open the output file for writing
f = file(fs, 'w')
progress.Update(0, _('Writing Headers'))
# Importing Definitions from XMLExport
XMLExportObject = XMLExport.XMLExport(self, -1, '')
# Writing XML's DTD Headers
XMLExportObject.WritingXMLDTD(f)
# Writing Library Records
progress.Update(9, _('Writing Library Records'))
seriesList = []
if db != None:
dbCursor = db.cursor()
if self.seriesNum <> 0:
SQLText = """SELECT SeriesNum, SeriesID, SeriesComment, SeriesOwner, DefaultKeywordGroup
FROM Series2
WHERE SeriesNum = %s"""
dbCursor.execute(SQLText, self.seriesNum)
if dbCursor.rowcount > 0:
f.write(' <SeriesFile>\n')
XMLExportObject.WritingSeriesRecords(f, dbCursor)
if dbCursor.rowcount > 0:
f.write(' </SeriesFile>\n')
if self.episodeNum <> 0:
SQLText = """SELECT a.SeriesNum, SeriesID, SeriesComment, SeriesOwner, DefaultKeywordGroup
FROM Series2 a, Episodes b
WHERE a.SeriesNum = b.SeriesNum
AND b.EpisodeNum = %s"""
dbCursor.execute(SQLText, self.episodeNum)
if dbCursor.rowcount > 0:
f.write(' <SeriesFile>\n')
XMLExportObject.WritingSeriesRecords(f, dbCursor)
if dbCursor.rowcount > 0:
f.write(' </SeriesFile>\n')
if self.collectionNum <> 0:
SQLText = """SELECT a.SeriesNum, SeriesID, SeriesComment, SeriesOwner, DefaultKeywordGroup
FROM Series2 a, Episodes b, Clip c, Collect d
WHERE a.SeriesNum = b.SeriesNum
AND b.EpisodeNum = c.EpisodeNum
AND c.CollectNum = d.CollectNum
AND d.CollectNum = %s"""
dbCursor.execute(SQLText, self.collectNum)
if dbCursor.rowcount > 0:
f.write(' <SeriesFile>\n')
XMLExportObject.WritingSeriesRecords(f, dbCursor)
if dbCursor.rowcount > 0:
f.write(' </SeriesFile>\n')
# Populating list with episodes
for seriesRec in dbCursor.fetchall():
if seriesRec not in seriesList:
seriesList.append(seriesRec[0])
dbCursor.close()
if DEBUG:
print "Library Records:", seriesList
# Writing Episode Records
progress.Update(18, _('Writing Episode Records'))
episodesList = []
if db != None:
dbCursor = db.cursor()
SQLText = """SELECT EpisodeNum, EpisodeID, SeriesNum, TapingDate, MediaFile, EpLength, EpComment
FROM Episodes2
WHERE SeriesNum = %s"""
# episodes = FakeCursorObject()
dbCursor.execute(SQLText, seriesRec[0])
if dbCursor.rowcount > 0:
f.write(' <EpisodeFile>\n')
XMLExportObject.WritingEpisodeRecords(f, dbCursor)
if dbCursor.rowcount > 0:
f.write(' </EpisodeFile>\n')
# Populating list with episodes
for episodeRec in dbCursor.fetchall():
if episodeRec not in episodesList:
episodesList.append(episodeRec[0])
if DEBUG:
print "Episode Records:", episodesList
dbCursor.close()
# Writing Core Data Records
progress.Update(27, _('Writing Core Data Records'))
if db != None:
dbCursor = db.cursor()
SQLText = """SELECT CoreDataNum, Identifier, Title, Creator, Subject, Description, Publisher, Contributor, DCDate, DCType, Format, Source, Language, Relation, Coverage, Rights
FROM CoreData2
WHERE Identifier = 'Volume.mpg'"""
dbCursor.execute(SQLText)
if dbCursor.rowcount > 0:
f.write(' <CoreDataFile>\n')
XMLExportObject.WritingCoreDataRecords(f, dbCursor)
if dbCursor.rowcount > 0:
f.write(' </CoreDataFile>\n')
dbCursor.close()
# Writing Collection Records
progress.Update(36, _('Writing Collection Records'))
collectionsList = []
if db != None:
dbCursor = db.cursor()
SQLText = """SELECT a.CollectNum, CollectID, ParentCollectNum, CollectComment, CollectOwner, a.DefaultKeywordGroup
FROM Collections2 a, Clips2 b
WHERE a.CollectNum = b.CollectNum AND
b.EpisodeNum = %s"""
collections = FakeCursorObject()
dbCursor.execute(SQLText, episodeRec[0])
# Populating list with episodes
for collectionRec in dbCursor.fetchall():
print collectionRec
print collectionsList
print (collectionRec[0], collectionRec[1]) not in collectionsList
print
if (collectionRec[0], collectionRec[1]) not in collectionsList:
collectionsList.append((collectionRec[0], collectionRec[1]))
collections.append(collectionRec)
if dbCursor.rowcount > 0:
f.write(' <CollectionFile>\n')
XMLExportObject.WritingCollectionRecords(f, collections)
if dbCursor.rowcount > 0:
f.write(' </CollectionFile>\n')
if DEBUG:
print "Collection Recs:", collectionsList
dbCursor.close()
#Writing Clip Records
progress.Update(45, _('Writing Clip Records'))
clipsList = []
if db != None:
dbCursor = db.cursor()
SQLText = """SELECT ClipNum, ClipID, CollectNum, a.EpisodeNum, a.MediaFile, ClipStart, ClipStop, ClipComment, SortOrder
FROM Clips2 a, Episodes2 b
WHERE a.EpisodeNum = %s"""
# clips = FakeCursorObject()
dbCursor.execute(SQLText, episodeRec[0])
if dbCursor.rowcount > 0:
f.write(' <ClipFile>\n')
XMLExportObject.WritingClipRecords(f, dbCursor)
if dbCursor.rowcount > 0:
f.write(' </ClipFile>\n')
# Populating list with clips
for clipRec in dbCursor.fetchall():
if clipRec not in clipsList:
clipsList.append(clipRec[0])
if DEBUG:
print "Clip Recs:", clipsList
dbCursor.close()
#Writing Transcript Records
transcriptsList = []
progress.Update(54, _('Writing Transcript Records (This will seem slow because of the size of the Transcript Records.)'))
if db != None:
dbCursor = db.cursor()
#Querying all transcripts based on Episodes
SQLText1 = """SELECT TranscriptNum, TranscriptID, EpisodeNum, SourceTranscriptNum, ClipNum, SortOrder, Transcriber, ClipStart, ClipStop, Comment, RTFText
FROM Transcripts2
WHERE EpisodeNum = %s
AND ClipNum = 0"""
#Querying all transcripts based on Clips
SQLText2 = """SELECT TranscriptNum, TranscriptID, EpisodeNum, SourceTranscriptNum, ClipNum, SortOrder, Transcriber, ClipStart, ClipStop, Comment, RTFText
FROM Transcripts2
WHERE ClipNum = %s"""
if DEBUG:
print "Selecting Transcripts"
# transcripts = FakeCursorObject()
# Adding all transcripts based on episodes to the list of all transcripts
for episodeRec in episodesList:
dbCursor.execute(SQLText1, episodeRec)
for record in dbCursor.fetchall():
transcriptsList.append(record)
# Adding all transcripts based on clips to the list of all transcripts
for clipRec in clipsList:
dbCursor.execute(SQLText2, clipRec)
for record in dbCursor.fetchall():
transcriptsList.append(record)
if DEBUG:
print "%d Transcripts selected." % dbCursor.rowcount
if dbCursor.rowcount > 0:
f.write(' <TranscriptFile>\n')
#Writing all transcripts into the xml file
XMLExportObject.WritingTranscriptRecords(f, dbCursor, progress)
if dbCursor.rowcount > 0:
f.write(' </TranscriptFile>\n')
if DEBUG:
print
print transcriptsList
dbCursor.close()
# Collecting ClipKeyword data
clipKeywordsList = []
keywordsList = []
# Collecting ClipKeywords from Episodes
# Iterate through the Episode list...
for episodeRec in episodesList:
if DEBUG:
print
print "episodeRec =", episodeRec
# ... add each episode's keyword to the episodeClipKeywords list...
episodeClipKeywords = DBInterface.list_of_keywords(Episode = episodeRec)
if DEBUG:
print
print "Episode ClipKeywords =", episodeClipKeywords
# ... and add this list to the actual ClipKeyword list.
for episodeClip in episodeClipKeywords:
if episodeClip not in clipKeywordsList:
clipKeywordsList.append(episodeClip)
for clipKeyword in clipKeywordsList:
if DEBUG:
print
print clipKeyword[0], clipKeyword[1]
# If the keyword isn't already in in the Keyword List...
if (clipKeyword[0], clipKeyword[1]) not in keywordsList:
# ... add the keyword to the Keyword List.
keywordsList.append((clipKeyword[0], clipKeyword[1]))
if DEBUG:
print
print "Keword List =", keywordsList
# Collecting ClipKeywords from Clips
# Iterate through the Clip List...
for clipRec in clipsList:
if DEBUG:
print
print "clipRec =", clipRec
# ... add each clip's keyword to the clipClipKeywords list
clipClipKeywords = DBInterface.list_of_keywords(Clip = clipRec)
if DEBUG:
print
print "Clip ClipKeywords =", clipClipKeywords
# ... and add this to the actual ClipKeyword list.
for clipClipKeyword in clipClipKeywords:
if clipClipKeyword not in clipKeywordsList:
clipKeywordsList.append(clipClipKeyword)
for clipKeyword in clipKeywordsList:
if DEBUG:
print
print clipKeyword[0], clipKeyword[1]
# If the keyword isn't already in the Keyword List...
if (clipKeyword[0], clipKeyword[1]) not in keywordsList:
# ... add the keyword to the Keyword List.
keywordsList.append((clipKeyword[0], clipKeyword[1]))
if DEBUG:
print
print "Keyword List =", keywordsList
# Writing Keyword Records
progress.Update(63, _('Writing Keyword Records'))
if db != None:
dbCursor = db.cursor()
SQLText = """SELECT KeywordGroup, Keyword, Definition
FROM Keywords2
WHERE KeywordGroup = %s
AND Keyword = %s"""
allKeywords = FakeCursorObject()
for clipKeyword in keywordsList:
dbCursor.execute(SQLText, (clipKeyword[0], clipKeyword[1]))
for record in dbCursor.fetchall():
allKeywords.append(record)
if dbCursor.rowcount > 0:
f.write(' <KeywordFile>\n')
XMLExportObject.WritingKeywordRecords(f, allKeywords)
if dbCursor.rowcount > 0:
f.write(' </KeywordFile>\n')
dbCursor.close()
# Writing ClipKeyword Records
progress.Update(72, _('Writing Clip Keyword Records'))
if db != None:
dbCursor = db.cursor()
SQLText = """SELECT EpisodeNum, ClipNum, KeywordGroup, Keyword, Example
FROM ClipKeywords2
WHERE KeywordGroup = %s
AND Keyword = %s"""
allClipKeywords = FakeCursorObject()
for clipKeyword in clipKeywordsList:
dbCursor.execute(SQLText, (clipKeyword[0], clipKeyword[1]))
for record in dbCursor.fetchall():
allClipKeywords.append(record)
if dbCursor.rowcount > 0:
f.write(' <ClipKeywordFile>\n')
XMLExportObject.WritingClipKeywordRecords(f, allClipKeywords)
if dbCursor.rowcount > 0:
f.write(' </ClipKeywordFile>\n')
dbCursor.close()
# Collecting Note data
notesList = []
# Collecting NoteData from Library...
for seriesRec in seriesList:
seriesNotesList = DBInterface.list_of_notes(Library = seriesRec)
if DEBUG:
print
print "Library Notes List =", seriesNotesList
for seriesNote in seriesNotesList:
# If the note isn't already in the notesList...
if seriesNote not in notesList:
# ... add the note to the notesList.
notesList.append(seriesNote)
# Collecting NoteData from Episodes
# Iterate through the Episode list...
for episodeRec in episodesList:
# ... add each episode's note to the episodeNoteList...
episodeNotesList = DBInterface.list_of_notes(Episode = episodeRec)
if DEBUG:
print
print "Episode Note List =", episodeNotesList
for episodeNote in episodeNotesList:
# If the note isn't already in the Note List...
if episodeNote not in notesList:
# ... add the note to the Note List.
notesList.append(episodeNote)
# Collecting NoteData from Collections
# Iterate through the Collection list...
for collectionRec in collectionsList:
# ... add each collection's note to the collectionNoteList...
collectionNotesList = DBInterface.list_of_notes(Collection = collectionRec[0])
for collectionNote in collectionNotesList:
# If the note isn't alreadz in the Note List...
if collectionNote not in notesList:
# ... add the note to the Note List
notesList.append(collectionNote)
if DEBUG:
print
print "Collection Note List =", collectionNotesList
if DEBUG:
print
print "Note List =", notesList
progress.Update(81, _('Writing Note Records'))
if db != None:
dbCursor = db.cursor()
SQLText = """SELECT NoteNum, NoteID, SeriesNum, EpisodeNum, CollectNum, ClipNum, TranscriptNum, NoteTaker, NoteText
FROM Notes2
WHERE NoteID = %s"""
allNotes = FakeCursorObject()
for note in notesList:
dbCursor.execute(SQLText, note)
for record in dbCursor.fetchall():
allNotes.append(record)
if dbCursor.rowcount > 0:
f.write(' <NoteFile>\n')
XMLExportObject.WritingNoteRecords(f, allNotes)
if dbCursor.rowcount > 0:
f.write(' </NoteFile>\n')
dbCursor.close()
XMLExportObject.Destroy()
except:
if 'unicode' in wx.PlatformInfo:
# Encode with UTF-8 rather than TransanaGlobal.encoding because this is a prompt, not DB Data.
prompt = unicode(_('An error occurred during Selective Data Export.\n%s\n%s'), 'utf8')
else:
prompt = _('An error occurred during Selective Data Export.\n%s\n%s')
errordlg = Dialogs.ErrorDialog(self, prompt % (sys.exc_info()[0], sys.exc_info()[1]))
errordlg.ShowModal()
errordlg.Destroy()
if DEBUG:
import traceback
traceback.print_exc(file=sys.stdout)
dbCursor.close()
f.close()
progress.Update(100)
progress.Destroy()
def run_plugin(self, plugin_cls, **kwargs):
"""Runs plugin of specified class plugin_cls on current data set,
replaces current data and refreshes plot"""
cfg = None
# Instantiate the plugin to see if it has a self.config dict
# that should be configured by the user prior to execution
plugin_instance = plugin_cls()
if hasattr(plugin_instance, "config"):
cfg = self.configure_plugin_dlg(plugin_instance)
if cfg is None:
return
try:
plugin_process, plugin_queue, exception_queue = mainmodel.run_plugin(
plugin_cls, self.data, cfg, **kwargs)
except MemoryError as err: # Insufficient memory to run plugin with current data
err_dlg = wx.MessageDialog(
self.view,
message="Insufficient memory to run plugin.",
caption="Unable To Run Plugin",
style=wx.ICON_ERROR)
err_dlg.ShowModal()
err_dlg.Destroy()
return
keepGoing = True
try:
progress_dlg = wx.ProgressDialog(
"Running Plugin",
"Please wait, executing plugin...",
parent=self.view,
style=wx.PD_CAN_ABORT)
while keepGoing:
wx.MilliSleep(125)
(keepGoing, skip) = progress_dlg.UpdatePulse()
try:
if not plugin_process.is_alive():
# Catch low-level exceptions thrown by multiprocessing, such as MemoryError
# exceptions raised when attempting to send data through the queue
module_logger.error(
"Unknown error occurred during plugin execution, plugin terminated"
)
err_msg = ' '.join([
"An unknown error has occurred running the plugin.",
"Please ensure your system has sufficient memory and disk space to process this data.",
"If the problem persists, please contact the plugin's author."
])
err_dlg = wx.MessageDialog(
self.view,
message=err_msg,
caption="Unable To Run Plugin",
style=wx.ICON_ERROR)
err_dlg.ShowModal()
err_dlg.Destroy()
break
exc_type, exc = exception_queue.get(block=False)
err_str = str(exc)
if len(err_str) == 0:
err_str = exc_type.__name__
module_logger.error(
"Error occurred running plugin: {0}".format(err_str))
err_msg = "An error occurred while running the plugin:\n{0}".format(
err_str)
err_dlg = wx.MessageDialog(self.view,
message=err_msg,
caption="Unable To Run Plugin",
style=wx.ICON_ERROR)
err_dlg.ShowModal()
err_dlg.Destroy()
break
except Queue.Empty:
pass
try:
returned_data = plugin_queue.get(False)
except Queue.Empty:
continue
if returned_data is not None:
self.model.data = returned_data
break
if not keepGoing:
break
wx.getApp().Yield()
finally:
plugin_process.join()
progress_dlg.Destroy()
def __init__(self,
parent,
properties=None,
show_controls=True,
size=(600, 600),
loadData=True,
**kwargs):
wx.Frame.__init__(self,
parent,
-1,
size=size,
title='Dimensionality Reduction Plot',
**kwargs)
self.SetName('Plot main')
if properties is not None:
global p
p = properties
if not p.is_initialized():
logging.critical(
'Classifier requires a properties file. Exiting.')
raise Exception(
'Classifier requires a properties file. Exiting.')
global db
db = DBConnect.getInstance()
global classifier
classifier = parent
if loadData:
# Define a progress dialog
dlg = wx.ProgressDialog(
'Fetching cell data...', '0% Complete', 100, classifier,
wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME
| wx.PD_REMAINING_TIME | wx.PD_CAN_ABORT)
def cb(frac):
cont, skip = dlg.Update(int(frac * 100.),
'%d%% Complete' % (frac * 100.))
if not cont: # cancel was pressed
dlg.Destroy()
raise StopCalculating()
# Load the data for each object
try:
self.data, self.data_dic = self.load_obj_measurements(cb)
except StopCalculating:
self.PostMessage('User canceled updating training set.')
return
dlg.Destroy()
else:
self.data, self.data_dic = None, None
self.features_dic = self.load_feature_names()
self.class_masks = None
self.class_names = None
self.object_opacity = None
figpanel = PlotNotebook(self)
self.figure_scores = figpanel.add('Scores')
self.figure_loadings = figpanel.add('Loadings')
self.update_figures()
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(figpanel, 1, wx.EXPAND)
configpanel = PlotControl(self, self.figure_scores,
self.figure_loadings)
sizer.Add(configpanel, 0, wx.EXPAND | wx.ALL, 5)
self.SetSizer(sizer)
self.Centre()
def merge_files(destination, sources, force_headless=False):
is_headless = force_headless or get_headless()
if not is_headless:
import wx
if len(sources) == 0:
return
if not is_headless:
progress = wx.ProgressDialog(
"Writing " + destination,
"Loading " + sources[0],
maximum=len(sources) * 4 + 1,
style=wx.PD_CAN_ABORT
| wx.PD_APP_MODAL
| wx.PD_ELAPSED_TIME
| wx.PD_REMAINING_TIME,
)
count = 0
try:
pipeline = cpp.Pipeline()
has_error = [False]
def callback(caller, event):
if isinstance(event, cpp.LoadExceptionEvent):
has_error = True
wx.MessageBox(
message="Could not load %s: %s" % (sources[0], event.error),
caption="Failed to load %s" % sources[0],
)
has_error[0] = True
pipeline.add_listener(callback)
pipeline.load(sources[0])
if has_error[0]:
return
if destination.lower().endswith(".h5"):
mdest = cpmeas.Measurements(filename=destination, multithread=False)
h5_dest = True
else:
mdest = cpmeas.Measurements(multithread=False)
h5_dest = False
for source in sources:
if not is_headless:
count += 1
keep_going, skip = progress.Update(count, "Loading " + source)
if not keep_going:
return
if h5py.is_hdf5(source):
msource = cpmeas.Measurements(
filename=source, mode="r", multithread=False
)
else:
msource = cpmeas.load_measurements(source)
dest_image_numbers = mdest.get_image_numbers()
source_image_numbers = msource.get_image_numbers()
if len(dest_image_numbers) == 0 or len(source_image_numbers) == 0:
offset_source_image_numbers = source_image_numbers
else:
offset_source_image_numbers = (
np.max(dest_image_numbers)
- np.min(source_image_numbers)
+ source_image_numbers
+ 1
)
for object_name in msource.get_object_names():
if object_name in mdest.get_object_names():
destfeatures = mdest.get_feature_names(object_name)
else:
destfeatures = []
for feature in msource.get_feature_names(object_name):
if object_name == cpmeas.EXPERIMENT:
if not mdest.has_feature(object_name, feature):
src_value = msource.get_experiment_measurement(feature)
mdest.add_experiment_measurement(feature, src_value)
continue
src_values = msource.get_measurement(
object_name, feature, image_set_number=source_image_numbers
)
mdest[
object_name, feature, offset_source_image_numbers
] = src_values
destset = set(destfeatures)
if not is_headless:
keep_going, skip = progress.Update(
count + 1, "Saving to " + destination
)
if not keep_going:
return
if not h5_dest:
pipeline.save_measurements(destination, mdest)
finally:
if not is_headless:
progress.Destroy()
def read_videos_for_length(self):
self.cap = cv2.VideoCapture(self.video_list_with_address[self.index_video][:-1])
success, image = self.cap.read()
count = 0
# get preferences in textbox annotation panel
start = int(self.annotation.get_Text(1))
end = int(self.annotation.get_Text(2))
self.address = os.path.dirname(self.config)
if not os.path.isdir(self.address + os.sep + self.name):
os.mkdir(self.address + os.sep + self.name)
num_frame_annotated = int(self.annotation.get_Text(3))
num_frame_automatic = int(self.annotation.get_Text(4))
my_list = list(range(start,
end)) # list of integers from 1 to end # adjust this boundaries to fit your needs
random.shuffle(my_list)
if num_frame_annotated < (end - start):
if self.import_from_deeplabcut_flag:
frames = self.annotation.Get_annotation_for_deeplabcut_compat()
else:
frames = my_list[0:num_frame_annotated]
if num_frame_automatic + num_frame_annotated<(end - start):
frames_annotated = my_list[num_frame_annotated:num_frame_automatic + num_frame_annotated]
else:
wx.MessageBox('Please enter a number of frames to automatically annotate <= to the total number of selected frames (end-start)\n'
'Number of frame to annotate too high\n '
'User Input Error'
, 'Error!', wx.OK | wx.ICON_ERROR)
self.error = 1
return
else:
wx.MessageBox('Please enter a number of frames to annotate <= to the total number of selected frames (end-start)\n'
'Number of frame to annotate too high\n '
'User Input Error'
, 'Error!', wx.OK | wx.ICON_ERROR)
self.error = 1
return
address = os.path.dirname(self.annotation.config)
p = open(os.path.join(address,self.video_list_with_address[self.index_video][
self.find(self.video_list_with_address[self.index_video], os.sep)[-1] + 1:-1]+ '_index_annotation.txt'), 'w')
p2 = open(os.path.join(address, self.video_list_with_address[self.index_video][
self.find(self.video_list_with_address[self.index_video], os.sep)[-1] + 1:-1] + '_index_annotation_auto.txt'), 'w')
for i in frames:
p.writelines(str(i))
p.writelines('\n')
for i in frames_annotated:
p2.writelines(str(i))
p2.writelines('\n')
p.close()
p2.close()
else:
permission = wx.MessageBox(
"Frame already extracted\n"
"Do you want to extract frames again? (The procedure will delete previous frames", "Confirm",
wx.YES_NO | wx.NO_DEFAULT, self)
if permission == 2:
shutil.rmtree(self.address + os.sep + self.name)
try:
os.remove(self.address + os.sep + "Annotation_" + self.video_list_with_address[self.index_video][
self.find(self.video_list_with_address[self.index_video], os.sep)[-1] + 1:-1] + '_' + self.scorer[:-1] + '.csv')
os.remove(self.address + os.sep + "Annotation_" + self.video_list_with_address[self.index_video][
self.find(self.video_list_with_address[self.index_video], os.sep)[-1] + 1:-1] + '_' + self.scorer[:-1])
except:
pass
os.mkdir(self.address + os.sep + self.name)
num_frame_annotated = int(self.annotation.get_Text(3))
num_frame_automatic = int(self.annotation.get_Text(4))
my_list = list(range(start,
end)) # list of integers from 1 to 99 # adjust this boundaries to fit your needs
random.shuffle(my_list)
if num_frame_annotated < (end - start):
if self.import_from_deeplabcut_flag:
frames = self.annotation.Get_annotation_for_deeplabcut_compat()
else:
frames = my_list[0:num_frame_annotated]
if num_frame_automatic + num_frame_annotated < (end - start):
frames_annotated = my_list[num_frame_annotated:num_frame_automatic + num_frame_annotated]
else:
wx.MessageBox(
'Please enter a number of frames to automatically annotate <= to the total number of selected frames (end-start)\n'
'Number of frame to annotate too high\n '
'User Input Error'
, 'Error!', wx.OK | wx.ICON_ERROR)
self.error = 1
return
else:
wx.MessageBox(
'Please enter a number of frames to annotate <= to the total number of selected frames (end-start)\n'
'Number of frame to annotate too high\n '
'User Input Error'
, 'Error!', wx.OK | wx.ICON_ERROR)
self.error = 1
return
address = os.path.dirname(self.annotation.config)
p = open(os.path.join(address, self.video_list_with_address[self.index_video][
self.find(self.video_list_with_address[self.index_video], os.sep)[-1] + 1:-1] + '_index_annotation.txt'), 'w')
p2 = open(os.path.join(address, self.video_list_with_address[self.index_video][
self.find(self.video_list_with_address[self.index_video], os.sep)[-1] + 1:-1] + '_index_annotation_auto.txt'), 'w')
for i in frames:
p.writelines(str(i))
p.writelines('\n')
for i in frames_annotated:
p2.writelines(str(i))
p2.writelines('\n')
p.close()
p2.close()
else:
return
self.frames_id = np.asarray(range(start, end, 1)).astype(int)
progress = wx.ProgressDialog("extraction in progress", "please wait", maximum=100, parent=self,
style=wx.PD_SMOOTH | wx.PD_AUTO_HIDE)
self.processSents()
while success and count < start:
count += 1
success, image = self.cap.read()
while success and count >= start and count < end:
cv2.imwrite(self.address + os.sep + self.name + os.sep + 'frame_' + ("{:04d}".format(count)) + '.png',
image)
progress.Update(int(count / len(self.frames_id)) * 100)
count += 1
success, image = self.cap.read()
progress.Destroy()
wx.Yield()
self.cap.release()
def XValidate(self, nPermutations):
# Make sure all data is available in the training set
if not self.classifier.UpdateTrainingSet():
return
# Initialize process dialog
def cb(frac):
cont, skip = dlg.Update(int(frac * 100.),
'%d%% Complete' % (frac * 100.))
if not cont: # Cancel was pressed
dlg.Destroy()
raise StopCalculating()
dlg = wx.ProgressDialog(
'Performing grid search for optimal parameters...', '0% Complete',
100, self.classifier, wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME
| wx.PD_REMAINING_TIME | wx.PD_CAN_ABORT)
# Define cross validation parameters
totalGroups = 5
trainingGroups = 4
# Convert the training set into SVM format and search for optimal parameters
# C and gamma using 5-fold cross-validation
logging.info(
'Performing grid search for parameters C and gamma on entire training set...'
)
self.TranslateTrainingSet(self.classifier.trainingSet.label_matrix,
self.classifier.trainingSet.values)
C, gamma = self.ParameterGridSearch(callback=cb)
dlg.Destroy()
logging.info(
'Grid search completed. Found optimal C=%d and gamma=%f.' %
(C, gamma))
# Create the classifier and initialize misclassification storage
classifier = Pipeline([
('anova',
feature_selection.SelectPercentile(feature_selection.f_classif,
percentile=self.percentile)),
('svc', SVC(kernel='rbf', C=C, gamma=gamma, eps=0.1))
])
nObjects = self.classifier.trainingSet.label_matrix.shape[0]
subsetSize = np.ceil(nObjects / float(totalGroups))
indices = np.arange(nObjects)
misclassifications = [[] for i in range(nObjects)]
# Create group combinations and arrays of all labels and values
dt = ','.join('i' * trainingGroups)
trainingTotalGroups = list(
np.fromiter(combinations(range(totalGroups), trainingGroups),
dtype=dt,
count=-1))
#trainingTotalGroups = list(combinations(range(totalGroups), trainingGroups))
allLabels = np.array(self.svm_train_labels)
allValues = np.array(self.svm_train_values)
# For all permutations of the subsets train the classifier on 4 totalGroups and
# classify the remaining group for a number of random subsets
logging.info('Calculating average classification accuracy %d times over a ' \
'%0.1f%%/%0.1f%% cross-validation process' % \
(nPermutations, trainingGroups/float(totalGroups)*100, \
(1-trainingGroups/float(totalGroups))*100))
dlg = wx.ProgressDialog(
'Calculating average cross-validation accuracy...', '0% Complete',
100, self.classifier, wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME
| wx.PD_REMAINING_TIME | wx.PD_CAN_ABORT)
nTrainingTotalGroups = len(trainingTotalGroups)
nOperations = float(nPermutations * nTrainingTotalGroups)
for per in range(nPermutations):
# Split the training set into subsets
np.random.shuffle(indices)
lastGroupStart = (totalGroups - 1) * subsetSize
subsets = np.hsplit(indices[0:lastGroupStart], (totalGroups - 1))
subsets.append(indices[lastGroupStart:], )
for index, group in enumerate(trainingTotalGroups):
# Retrieve indices of all objects in the training set
trainingSet = np.hstack(
[subsets[i] for i in range(totalGroups) if i in group])
# Train a classifier on the subset
classifier.fit(allValues[trainingSet], allLabels[trainingSet])
# Predict the test set using the trained classifier
testSet = np.hstack(
[subsets[i] for i in range(totalGroups) if i not in group])
testLabels = classifier.predict(allValues[testSet])
# Store all misclassifications
[misclassifications[testSet[i]].append(testLabels[i]) \
for i in range(len(testLabels)) \
if testLabels[i] != allLabels[testSet][i]]
# Update progress dialog
cb((nTrainingTotalGroups * per + index) / nOperations)
# Calculate average classification accuracy
dlg.Destroy()
logging.info('Average Classification Accuracy: %f%%' % \
((1-len([item for sublist in misclassifications for item in sublist]) /\
float(nObjects * nPermutations))*100))
return misclassifications
def on_button(self, event):
if event.GetId() == ID_SAMPLE_BUTTON:
# try:
self.validate_input_ranges()
number = self.calc_number_samples()
sample_dialog = wx.MessageDialog(
self,
"Proceed with calculating " + str(number) + " samples?",
caption="Confirm sample size",
style=wx.ICON_QUESTION | wx.OK | wx.CANCEL,
)
if sample_dialog.ShowModal() == wx.ID_OK:
save_dialog = wx.FileDialog(
event.GetEventObject(),
message="Save sampled output",
wildcard="Tab separated values (*.tsv)|*.tsv",
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT,
)
if save_dialog.ShowModal() == wx.ID_OK:
# 1. Copy original parameter values
original_values = []
for setting in self.__module.visible_settings():
original_values.append(setting.get_value())
# 2. Sample input parameters
self.__sample_list = self.generate_parameter_samples()
# 3. Open output file and write headers
output_file = open(save_dialog.GetPath(), "w")
headers = ""
for i, setting in enumerate(
self.__module.visible_settings()):
# Do not write settings without values, ie, buttons etc
if setting.get_text() != "":
headers += setting.get_text()
if i < len(self.__module.visible_settings()) - 1:
headers += "\t"
headers += "\n"
output_file.write(headers)
# 4. Run pipeline once for each sample
# ~*~
self.Show(False)
progressDialog = wx.ProgressDialog(
parent=self,
title="Sampling parameters",
message="Run 1",
maximum=len(self.__sample_list),
)
size = progressDialog.GetSize()
size.SetWidth(2 * size.GetWidth())
progressDialog.SetSize(size)
# ~^~
for i, l in enumerate(self.__sample_list):
# print '\nStarting run ' + str(i+1) + '...'
for j, value in enumerate(l):
if value is not None:
setting_nr = self.__parameters_list[j][1]
setting = self.__module.setting(setting_nr)
setting.set_value(value)
# print str(setting.get_text()) + ' -> ' + str(setting.get_value())
# ~*~
progressDialog.Update(
i + 1,
newmsg="Executing run " + str(i + 1) + " of " +
str(len(self.__sample_list)),
)
# ~^~
# It's not very efficient to run the complete pipeline
# when only the last module's parameter values are
# different. However, this is the only way I can get
# the images to update correctly for the last module. Ie,
# when I don't prepare and run the pipeline from scratch
# for every different configuration of the last module,
# I get the images generated by the first run for every
# run.
# 4.1 Prepare to run pipeline
self.prepare_for_run()
# 4.2 Run modules
for module in self.__pipeline.modules():
if (module.get_module_num() <=
self.__module.get_module_num()):
self.run_module(module)
# 4.3 Save output
self.save_run_output(i, save_dialog.GetDirectory(),
output_file)
# This is the way to run headless, if only I could get at the images...
# self.stop_now = False
# running_pipeline = self.__pipeline.run_with_yield(
# run_in_background=False,
# status_callback=self.status_callback)
# while not self.stop_now:
# measurements = running_pipeline.next()
# print '...run completed.'
# 5. Close output file
output_file.close()
# ~*~
progressDialog.Destroy()
# ~^~
# 6. Set parameters back to original values and close window
for i, setting in enumerate(
self.__module.visible_settings()):
setting.set_value(original_values[i])
self.Close(True)
def CopyImages(self):
self.MyLog("Calling CopyImages", str(self.CurrentPatientID))
AllPNGFiles = os.listdir(
os.path.join(self.SettingsObj.ROOTPATH, "SavePNG"))
AllRAWFiles = os.listdir(
os.path.join(self.SettingsObj.ROOTPATH, "SaveRaw"))
mess = "Transfering images ..."
Nb = len(AllPNGFiles) + len(AllRAWFiles)
if len(AllPNGFiles) > 2 or len(
AllRAWFiles
) > 2 and self.CurrentPatientID != 'none' and self.CurrentPatientID != 'ID':
dialog = wx.ProgressDialog("Clinical",
mess,
Nb,
style=wx.PD_ELAPSED_TIME
| wx.PD_REMAINING_TIME
| wx.PD_AUTO_HIDE)
count = 0
if os.path.isdir(
os.path.join(self.SettingsObj.ROIPATH,
"SavedImages")) == False:
os.mkdir(os.path.join(self.SettingsObj.ROIPATH, "SavedImages"))
if os.path.isdir(
os.path.join(self.SettingsObj.ROIPATH, "SavedImages",
self.CurrentPatientID)) == False:
os.mkdir(
os.path.join(self.SettingsObj.ROIPATH, "SavedImages",
self.CurrentPatientID))
DT = datetime.now()
DTTag = str(DT.year) + "-" + str(DT.month) + "-" + str(
DT.day) + "_" + str(DT.hour) + "h" + str(
DT.minute) + "m" + str(DT.second) + "s"
if not os.path.isdir(
os.path.join(self.SettingsObj.ROIPATH, "SavedImages",
self.CurrentPatientID, DTTag)):
os.mkdir(
os.path.join(self.SettingsObj.ROIPATH, "SavedImages",
self.CurrentPatientID, DTTag))
self.MyLog(
"CopyImages",
str(
os.path.join(self.SettingsObj.ROIPATH, "SavedImages",
self.CurrentPatientID, DTTag)))
if self.SettingsObj.SAVEPNG:
if not os.path.isdir(
os.path.join(self.SettingsObj.ROIPATH, "SavedImages",
self.CurrentPatientID, DTTag, "SavePNG")):
os.mkdir(
os.path.join(self.SettingsObj.ROIPATH, "SavedImages",
self.CurrentPatientID, DTTag, "SavePNG"))
try:
for r, d, f in os.walk(
os.path.join(self.SettingsObj.ROOTPATH,
"SavePNG")):
for file in f:
shutil.copy(
os.path.join(self.SettingsObj.ROOTPATH,
"SavePNG", file),
os.path.join(self.SettingsObj.ROIPATH,
"SavedImages",
self.CurrentPatientID, DTTag,
"SavePNG", file))
if os.path.isfile(
os.path.join(self.SettingsObj.ROIPATH,
"SavedImages",
self.CurrentPatientID, DTTag,
"SavePNG", file)):
os.remove(
os.path.join(self.SettingsObj.ROOTPATH,
"SavePNG", file))
count += 1
dialog.Update(count)
except:
pass
if self.SettingsObj.SAVERAW:
if not os.path.isdir(
os.path.join(self.SettingsObj.ROIPATH, "SavedImages",
self.CurrentPatientID, DTTag, "SaveRaw")):
os.mkdir(
os.path.join(self.SettingsObj.ROIPATH, "SavedImages",
self.CurrentPatientID, DTTag, "SaveRaw"))
try:
for r, d, f in os.walk(
os.path.join(self.SettingsObj.ROOTPATH,
"SaveRaw")):
for file in f:
shutil.copy(
os.path.join(self.SettingsObj.ROOTPATH,
"SaveRaw", file),
os.path.join(self.SettingsObj.ROIPATH,
"SavedImages",
self.CurrentPatientID, DTTag,
"SaveRaw", file))
if os.path.isfile(
os.path.join(self.SettingsObj.ROIPATH,
"SavedImages",
self.CurrentPatientID, DTTag,
"SaveRaw", file)):
os.remove(
os.path.join(self.SettingsObj.ROOTPATH,
"SaveRaw", file))
count += 1
dialog.Update(count)
except:
pass
dialog.Destroy()
def OnStart(self, event): if (not self.Validate()): return res = self.li.OnStart() if not res: return if not self.checkAsc(): return self.bc = self.bcckb.GetValue() sunlon = float(self.sundeg.GetValue()) if self.useminckb.GetValue(): sunlon += float(self.sunmin.GetValue())/60.0 if self.usesecckb.GetValue(): sunlon += float(self.sunsec.GetValue())/3600.0 sunretr = False moonlon = float(self.moondeg.GetValue()) if self.useminckb.GetValue(): moonlon += float(self.moonmin.GetValue())/60.0 if self.usesecckb.GetValue(): moonlon += float(self.moonsec.GetValue())/3600.0 moonretr = False mercurylon = float(self.mercurydeg.GetValue()) if self.useminckb.GetValue(): mercurylon += float(self.mercurymin.GetValue())/60.0 if self.usesecckb.GetValue(): mercurylon += float(self.mercurysec.GetValue())/3600.0 mercuryretr = self.mercuryretr.GetValue() venuslon = float(self.venusdeg.GetValue()) if self.useminckb.GetValue(): venuslon += float(self.venusmin.GetValue())/60.0 if self.usesecckb.GetValue(): venuslon += float(self.venussec.GetValue())/3600.0 venusretr = self.venusretr.GetValue() marslon = float(self.marsdeg.GetValue()) if self.useminckb.GetValue(): marslon += float(self.marsmin.GetValue())/60.0 if self.usesecckb.GetValue(): marslon += float(self.marssec.GetValue())/3600.0 marsretr = self.marsretr.GetValue() jupiterlon = float(self.jupiterdeg.GetValue()) if self.useminckb.GetValue(): jupiterlon += float(self.jupitermin.GetValue())/60.0 if self.usesecckb.GetValue(): jupiterlon += float(self.jupitersec.GetValue())/3600.0 jupiterretr = self.jupiterretr.GetValue() saturnlon = float(self.saturndeg.GetValue()) if self.useminckb.GetValue(): saturnlon += float(self.saturnmin.GetValue())/60.0 if self.usesecckb.GetValue(): saturnlon += float(self.saturnsec.GetValue())/3600.0 saturnretr = self.saturnretr.GetValue() useascmc = self.useascmcckb.GetValue() asclon = float(self.ascdeg.GetValue())+float(self.ascmin.GetValue())/60.0+float(self.ascsec.GetValue())/3600.0 mclon = float(self.mcdeg.GetValue())+float(self.mcmin.GetValue())/60.0+float(self.mcsec.GetValue())/3600.0 useapprox = self.useapproxckb.GetValue() approxdeg = float(self.approxdeg.GetValue()) approxmin = float(self.approxmin.GetValue()) approxsec = float(self.approxsec.GetValue()) ftdata = ((sunlon, sunretr), (moonlon, moonretr), (mercurylon, mercuryretr), (venuslon, venusretr), (marslon, marsretr), (jupiterlon, jupiterretr), (saturnlon, saturnretr)) usemin = self.useminckb.GetValue() usesec = self.usesecckb.GetValue() useretr = self.useretrckb.GetValue() ftdatause = (usemin, usesec, useretr) ftdataascmc = (useascmc, asclon, mclon) ftdataapprox = (useapprox, approxdeg, approxmin, approxsec) ########## self.suffix = '' self.progtxt = mtexts.txts['BusyInfo2'] self.progbar = wx.ProgressDialog(mtexts.txts['Calculating'], self.progtxt+'\n', parent=self, style = wx.PD_CAN_ABORT|wx.PD_APP_MODAL|wx.PD_ELAPSED_TIME) self.progbar.Fit() self.btnShow.Enable(False) self.found = False if self.ar != None: del self.ar self.ar = None self.ftready = False self.abort = AbortFindTime() thId = thread.start_new_thread(self.calcCharts, (self.bc, ftdata, ftdatause, ftdataascmc, ftdataapprox, self)) self.timer = wx.Timer(self) self.Bind(wx.EVT_TIMER, self.OnTimer) self.timer.Start(500)
def InstallPluginFromFile(self, filenames):
info = []
try:
installed = []
for filename in filenames:
wzip = zipfile.ZipFile(filename, 'r')
xml = wzip.open("%splugin.xml" % wzip.namelist()[0], 'r')
root = ElementTree.fromstring(xml.read())
xml.close()
name = root[0].text.replace(" ", "_")
if name in self._manager.names:
item = self._manager.names.index(name)
if self._manager.states[item] < 3 or self._manager.states[
item] == 6:
root2 = ElementTree.parse(
os.path.join(self._parent._app.userdatadir,
"plugins", name,
"plugin.xml")).getroot()
else:
root2 = ElementTree.parse(
os.path.join(wx.StandardPaths.Get().GetTempDir(),
self._manager.tempdirs[name],
"plugin.xml")).getroot()
if root2[1].text == root[1].text:
if self._manager.states[
item] < 3 or self._manager.states[item] == 6:
installed.append("%s %s" %
(root2[0].text, root2[1].text))
else:
self.HandleLinkEvent(name, 5, False)
wzip.close()
continue
else:
shutil.rmtree(
os.path.join(self._parent._app.userdatadir,
"plugins", name))
self._manager.states[item] = 3
self._manager.RemovePlugin(name)
self.restart.pop(item)
self.listbox.items.pop(item)
info.append((wzip, root, name))
if len(installed):
installed = "\n".join([" " * 4 + name for name in installed])
wx.MessageBox(
_("The following plugins are already installed:\n\n%s") %
installed, _("Plugin Manager"),
wx.ICON_EXCLAMATION | wx.OK, self)
if not len(info):
return
names = "\n".join([" " * 4 + item[1][0].text for item in info])
install = wx.MessageBox(
_("Are you sure you want to install the following plugins?\n\n%s"
) % names, _("Plugin Manager"), wx.ICON_QUESTION | wx.YES_NO,
self)
if install != wx.YES:
return
plugindir = os.path.join(self._parent._app.userdatadir, "plugins")
disabled = 0
for i in range(len(self._manager.names) - 1, -1, -1):
if self._manager.enabled[i] or self._manager.states[i] == 1:
break
disabled += 1
names = self._manager.names[:]
if disabled > 0:
names = names[:-disabled]
if len(info) > 1:
dialog = wx.ProgressDialog("Write++", "", len(info))
i = 0
for wzip, root, name in info:
if len(info) > 1:
dialog.Update(i, _("Installing %s...") % root[0].text)
i += 1
wzip.extractall(plugindir)
names.append(name)
names.sort()
item = names.index(name)
self._manager.names.insert(item, name)
self._manager.enabled.insert(item, True)
restart = root[3].text == "True"
self._manager.LoadPlugin(name, not restart, item)
text = "<font><b>%s</b> %s<br>%s</font><div align=right>" % (
root[0].text, root[1].text, root[2].text)
if hasattr(self._manager.plugins[item], "OnInstall"):
self._manager.plugins[item].OnInstall()
if restart:
text2 = _(
"<font color=green>This plugin will be installed when you restart Write++. <a href=';4'>Restart Now</a> <a href='%s;5'>Undo</a></font><br>"
) % name
text = text2 + text[:text.index("<div align=right>")]
self._manager.states.insert(
item, 6) # 6 = will be installed on restart
else:
if hasattr(self._manager.plugins[item], "OnNewFrame"):
for frame in self._manager._app.frames:
self._manager.plugins[item].OnNewFrame(frame)
if hasattr(self._manager.plugins[item], "OnEnable"):
self._manager.plugins[item].OnEnable()
if hasattr(self._manager.plugins[item], "OnOptions"):
text += _("<a href='%s;0'>Options</a> ") % name
text += _("<a href='%s;1'>Disable</a> ") % name + _(
"<a href='%s;3'>Remove</a>") % name + " </div>"
self._manager.states.insert(item, 0)
self.listbox.items.insert(item, text)
self.restart.insert(item, restart)
self.listbox.SetItemCount(len(self.listbox.items))
self.listbox.Refresh()
self.listbox.Update()
if len(info) > 1:
dialog.Destroy()
finally:
for item in info:
item[0].close()
def Calculation(self):
"""
Calucualtion of mathematical morpholgy on all results anova and PostHoc
TF = Number of consecutive Time frame entered by usr
Alpha = Statistical Thesjold Difine by usr
SpaceCont = Contigous space point define by usr
SpaceFiel File with 3d coodonate to determine distance
"""
ResultType={'Anova.GFP':'/Result/GFP/Anova','Anova.Electrodes':'/Result/All/Anova',
'PostHoc.GFP':'/Result/GFP/PostHoc','PostHoc.Electrodes':'/Result/All/PostHoc'}
self.CorrectedMask={}
for r in ResultType:
res=self.file.getNode(ResultType[r])
if len(res)>0:
ShapeOriginalData=self.file.getNode('/Shape').read()
# extrating infromion usefull
# used for user interface feed back
# number of terms in Anova or in PostHoc mulipled by the number of TF* number of space point muliply * 2(Erosion/Dilatation)
self.NbCalcul=2*ShapeOriginalData.prod()
#Dictionary Correction Anova Contain the mask of All Anova Mask Keys = statistical Condition name
self.dlg = wx.ProgressDialog(
'Multiple Test Correction for '+r,
'Calculation in progress : 0 %',
self.NbCalcul, parent=self.parent,
style=wx.PD_AUTO_HIDE | wx.PD_REMAINING_TIME)
self.dlg.SetSize((200, 130))
tmp={}
print(res)
for v in res:
self.n=0
FolderName=r.split('.')[0]
try:
os.mkdir(self.resultFolder+'\\'+FolderName)
except:
pass
P=v['P']
Name=v['StatEffect']
CorrectedMask={}
# adapt the conseutive number of time frame and the contigous criteria to the length o Data
# in case of the user made a mistake.
# if their is only one TF we cannot have a TF value !=1
# same remark for the contigous criteria
if P.shape[0]==1:
self.TF=1
else:
self.TF=self.TFDict[FolderName]
if P.shape[1] == 1:
self.SpaceCont = 1
else:
self.SpaceCont=self.SpaceContDict[FolderName]
# we compute an openning more restrictive that means errosion folwed by a dilatation
# the BinaryData is all the pvalue lower than Alpha
self.BinaryData=np.zeros(P.shape)
print('init')
print(self.AlphaDict[FolderName])
self.BinaryData[P<self.AlphaDict[FolderName]]=1
print(self.BinaryData.sum())
# Dilatation
self.__MathematicalMorphology__(Dilate=False)
# the BinaryData is the Mask the come from the errosion
self.BinaryData=self.Mask
# Erosion
self.__MathematicalMorphology__(Dilate=True)
tmp[Name]=self.Mask
# Corrected Mask is a Dicionary tha containe all the binarymask
self.CorrectedMask[r]=tmp
self.dlg.Destroy()
self.file.close()
def onAddEvidence(self, event):
try:
caseDetails
except NameError: #if caseDetails not defined
print("Case not opened")
else: #if caseDetails is defined
openFileDialog = wx.FileDialog(
self,
"Open",
"",
"",
"*.dd", #creates a filedialog that only allow user to select .dd files
wx.FD_OPEN | wx.FD_FILE_MUST_EXIST)
openFileDialog.ShowModal()
global caseDir, caseDbPath
evidencePath = openFileDialog.GetPath(
) #get path of selected dd file
fileName = os.path.basename(evidencePath)
for x in caseDetails:
caseDir = x[4] #get case directory from caseDetails
caseDbPath = x[5] #get case database path from caseDetails
evidenceDbDir = Path(caseDir + "/Evidence_Database")
if evidenceDbDir.is_dir() == False: #check if directory exist
os.mkdir(
str(evidenceDbDir)) #create directory if it does not exist
if fileName != "":
self._dialog = wx.ProgressDialog(
"Adding evidence",
"Creating database for '{s}'".format(s=fileName), 100)
LoadingDialog(self._dialog) #starts the loading dialog
load_db = subprocess.call([
"tsk_loaddb", "-d",
"{caseDir}/Evidence_Database/{fileName}.db".format(
caseDir=caseDir, fileName=fileName), evidencePath
]) #use tsk_loaddb to generate tsk database
LoadingDialog.endLoadingDialog(self) #ends the loading dialog
if load_db == 0: #if no error
conn = connectdb.create_connection(caseDbPath)
with conn:
evidenceDbPath = str(
evidenceDbDir) + "/" + fileName + ".db"
#hash = "md5sum {evidencePath} | awk '{col}".format(evidencePath=evidenceDbPath, col="{print $1}")
#evidenceMd5 = subprocess.Popen([hash], stdout=subprocess.PIPE).communicate()[0]
evidenceMd5 = "None"
insertEvidence = (1, fileName, evidenceDbPath,
datetime.datetime.now().strftime(
"%Y-%m-%d %H:%M:%S"),
evidenceMd5)
connectdb.insertEvidenceDetails(
conn, insertEvidence
) #insert to EvidenceInfo in case database
evidenceConn = connectdb.create_connection(
caseDir + "/Evidence_Database/" + fileName +
".db") #connect to tsk database
evidencePart = connectdb.select_image_partitions(
evidenceConn) #get image partitions from tsk database
if Path(caseDir +
"/Evidence_Database/Deleted_Files.db").is_file(
) == False: #check if Deleted_Files.db exist
createDeletedFilesDb = connectdb.create_connection(
caseDir + "/Evidence_Database/Deleted_Files.db")
deteledFilesTable = "CREATE TABLE 'DeletedFiles' ('fileType' TEXT, 'status' TEXT, 'inode' TEXT, 'filePath' TEXT, 'ctime' TEXT, 'crtime' TEXT, 'atime' TEXT, 'mtime' TEXT, 'size' INTEGER, 'uid' INTEGER, 'gid' INTEGER, 'image' TEXT);"
connectdb.createTable(
createDeletedFilesDb,
deteledFilesTable) #creates if it does not exist
else:
createDeletedFilesDb = connectdb.create_connection(
caseDir + "/Evidence_Database/Deleted_Files.db"
) #connects to Deleted_Files.db
for x in evidencePart:
if x[2] != "Unallocated":
subprocess.Popen(
[
"tsk_recover", "-e", "-o",
str(x[0]), evidencePath,
caseDir + "/Extracted/" + fileName
]
) #recover files from all partitions that re not unallocated
listAllDeletedFiles = "fls -rFdl -o {offset} {image}".format(
offset=str(x[0]), image=evidencePath)
process = subprocess.Popen(
listAllDeletedFiles,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE
) #list all deleted files
stdout, stderr = process.communicate()
output = stdout.decode()
chk = re.sub(
r'[ ]\*[ ]', '\t*\t', output
) #change all ' ' in the second and third column of fls output to to '\t'
chk = re.sub(r'\n', '\t',
chk) #change all '\n' to '\t'
chk = chk.split(
'\t'
) #splits all values between \t into a list
itemList = []
k = 0
for i in range(k, len(chk) - 1, 11):
k = i
itemList.append(
chk[k:k + 11]
) #appends every 11 items into a list
with createDeletedFilesDb:
for list in itemList:
insertDeletedFiles = (list[0], list[1],
list[2], list[3],
list[4], list[5],
list[6], list[7],
list[8], list[9],
list[10], fileName)
connectdb.insertDeletedFiles(
createDeletedFilesDb,
insertDeletedFiles
) #inserts all deleted files info into Deleted_Files.db
wx.MessageBox(
"Extracting '{file}' in the background.".format(
file=fileName))
global evidenceDetails
evidenceDetails = connectdb.select_evidence_details(conn)
self.auiNotebook.DeletePage(0)
self.auiNotebook.RemovePage(0)
self.addAuiTab("Summary", evidenceDetails)
self.recreateTree(caseDbPath)
openFileDialog.Destroy()