Develop Reference

canvasObjects; found PartInstance, expecting tuple in Abaqus/CAE

I'm developening an Abaqus/CAE plug-in, in this plug-in i'm using the gui toolkit, and i have a button that uses the PickStep, on click the button i can select a PartInstance in the viewport.
Then i want to export the selected PartInstance to an .obj file but when i try it, abaqus displays an error.
This is an example of my PICK BUTTON:
# PICK BUTTON 1
pickHf = FXHorizontalFrame(p=col2, opts=0, x=0, y=0, w=0, h=0, pl=0, pr=0, pt=0, pb=0, hs=DEFAULT_SPACING,
vs=DEFAULT_SPACING)
# Note: Set the selector to indicate that this widget should not be
# colored differently from its parent when the 'Color layout managers'
# button is checked in the RSG Dialog Builder dialog.
pickHf.setSelector(99)
label1 = FXLabel(p=pickHf, text='' + ' (None)', ic=None, opts=LAYOUT_CENTER_Y | JUSTIFY_LEFT)
pickHandler1 = DBPickHandler(form, form.uper, 'Select a 3D, discrete and dependent meshed instance', INSTANCES,
1, label1)
icon = afxGetIcon('select', AFX_ICON_SMALL)
FXButton(p=pickHf, text='\tPick Items in Viewport', ic=icon, tgt=pickHandler1, sel=AFXMode.ID_ACTIVATE,
opts=BUTTON_NORMAL | LAYOUT_CENTER_Y, x=0, y=0, w=0, h=0, pl=2, pr=2, pt=1, pb=1)
I save the value in an ObjectKeyword:
self.uper = AFXObjectKeyword(self.cmd, 'uper', True, pickedDefault)
This is how i export the PartInstance to .obj:
print 'Uper - ' + uper[0].name
f.write('Uper - '+uper[0].name+'\n')
session.writeOBJFile(fileName='C:/temp/Uper.obj', canvasObjects=(uper[0]))
That displays and error, and i also tried this:
print 'Fixed - ' + fixed[0].name
f.write(fixed[0].name+'\n')
fixedobj = open('Fixed.obj', 'w')
pickle.dump(fixed[0], fixedobj)
fixedobj.close()
But that does not work either.
I get this error:
canvasObjects;found PartInstance, expecting tuple

This answer will help you. On your call to session.writeOBJFile you are trying to create a one element tuple for the canvasObjects argument. Simply wrapping the item in parentheses won't achieve that. You need to add a comma to make it a tuple:
session.writeOBJFile(fileName='C:/temp/Uper.obj', canvasObjects=(uper[0],))
The Abaqus documentation says this about canvasObjects:
canvasObjects
A sequence of canvas objects to export.
I'm not sure if PartInstance is considered a canvas object or not, but you may still have problems even after correcting the argument to be a tuple. If so, make sure the items of the tuple are proper canvas objects.

How to solve Unicoder problem when reading csv

I am totally new to python. I am using a package that takes medical text and annotates it with classifiers called pyConTextNLP
It basically takes some natural language text, adds some 'modifiers' to it and classifies it whilst removing negative findings.
The problem I am having is how to add the list of modifiers as a csv or a yaml file. I have been following the basic setup instructions here:
The problem is the line here:
modifiers = itemData.get_items("https://raw.githubusercontent.com/chapmanbe/pyConTextNLP/master/KB/lexical_kb_05042016.yml")
itemData.get_items doesn't look like it exists anymore and there is a function instead called itemData.get_fileobj(). This takes a csv file as far as I understand and the csv is passed to the function markup.markItems(modifiers, mode="modifier") which looks at the text and 'marks up' any concepts in the raw text that match the modifiers.
The error that I get when trying to run the example code is:
if not `item.getLiteral() in compiledRegExprs:`
and this gives me the error:
AttributeError: 'UnicodeReader' object has no attribute 'getLiteral'
The whole code is here: but I have also written it below
import networkx as nx
import pyConTextNLP.itemData as itemData
import pyConTextNLP.pyConTextGraph as pyConText
reports = [
"""IMPRESSION: Evaluation limited by lack of IV contrast; however, no evidence of
bowel obstruction or mass identified within the abdomen or pelvis. Non-specific interstitial opacities and bronchiectasis seen at the right
base, suggestive of post-inflammatory changes.""",
"""DIAGNOSIS: NO SIGNIFICANT PATHOLOGY
MICRO These biopsies of large bowel mucosa show oedema of the lamina propriabut no architectural abnormality
There is no dysplasia or malignancy
There is no evidence of active inflammation
There is no increase in the inflammatory cell content of the lamina propria""" ,
"""IMPRESSION:
1. 2.0 cm cyst of the right renal lower pole. Otherwise, normal appearance
of the right kidney with patent vasculature and no sonographic evidence of
renal artery stenosis.
2. Surgically absent left kidney.""",
"""IMPRESSION: No definite pneumothorax""",
"""IMPRESSION: New opacity at the left lower lobe consistent with pneumonia."""
]
modifiers = itemData.get_fileobj("/Applications/anaconda3/lib/python3.7/site-packages/pyConTextNLP-0.6.2.0-py3.7.egg/pyConTextNLP/CSV_Modifiers.csv")
targets = itemData.get_fileobj("/Applications/anaconda3/lib/python3.7/site-packages/pyConTextNLP-0.6.2.0-py3.7.egg/pyConTextNLP/CSV_targets.csv")
def markup_sentence(s, modifiers, targets, prune_inactive=True):
"""
"""
markup = pyConText.ConTextMarkup()
markup.setRawText(s)
markup.cleanText()
markup.markItems(modifiers, mode="modifier")
markup.markItems(targets, mode="target")
markup.pruneMarks()
markup.dropMarks('Exclusion')
# apply modifiers to any targets within the modifiers scope
markup.applyModifiers()
markup.pruneSelfModifyingRelationships()
if prune_inactive:
markup.dropInactiveModifiers()
return markup
reports[3]
markup = pyConText.ConTextMarkup()
isinstance(markup,nx.DiGraph)
markup.setRawText(reports[4].lower())
print(markup)
print(len(markup.getRawText()))
markup.cleanText()
print(markup)
print(len(markup.getText()))
markup.markItems(modifiers, mode="modifier")
print(markup.nodes(data=True))
print(type(list(markup.nodes())[0]))
markup.markItems(targets, mode="target")
for node in markup.nodes(data=True):
print(node)
markup.pruneMarks()
for node in markup.nodes(data=True):
print(node)
print(markup.edges())
markup.applyModifiers()
for edge in markup.edges():
print(edge)
markItems function is here:
def markItems(self, items, mode="target"):
"""tags the sentence for a list of items
items: a list of contextItems"""
if not items:
return
for item in items:
self.add_nodes_from(self.markItem(item, ConTextMode=mode),
category=mode)
The question is, how can I get the code to read the list in the csv file without throwing this error?

Data frame text filtering with text

I need some help with running some filter on some data. I have a a data set made up of text. And i also have a list of words. I would like to filter each row of my data such that the remaining text in the rows will be made up of only words in the list object
words
(cell, CDKs, lung, mutations monomeric, Casitas, Background, acquired, evidence, kinases, small, evidence, Oncogenic )
data
ID Text
0 Cyclin-dependent kinases CDKs regulate a
1 Abstract Background Non-small cell lung
2 Abstract Background Non-small cell lung
3 Recent evidence has demonstrated that acquired
4 Oncogenic mutations in the monomeric Casitas
so after my filter i would like the data-frame to look like this
data
ID Text
0 kinases CDKs
1 Background cell lung
2 Background small cell lung
3 evidence acquired
4 Oncogenic mutations monomeric Casitas
I tried using the iloc and similar functions but I dont seem to get it. any help with that?

You can simply use apply() along with a simple list comprehension:
>>> df['Text'].apply(lambda x: ' '.join([i for i in x.split() if i in words]))
0 kinases CDKs
1 Background cell lung
2 Background cell lung
3 evidence acquired
4 Oncogenic mutations monomeric Casitas
Also, I made words a set to improve performance (O(1) average lookup time), I recommend you do the same.

I'm not certain this is the most elegant of solutions, but you could do:
to_remove = ['foo', 'bar']
df = pd.DataFrame({'Text': [
'spam foo& eggs',
'foo bar eggs bacon and lettuce',
'spam and foo eggs'
]})
df['Text'].str.replace('|'.join(to_remove), '')

2 different blocks of text are merging together. Can I separate them if i know what 1 is?

I've used a number of pdf-->text methods to extract text from pdf documents. For one particular type of PDF I have, neither pyPDF or pdfMiner are doing a good job extracting the text. However, http://www.convertpdftotext.net/ does it (almost) perfectly.
I discovered that the pdf I'm using has some transparent text in it, and it is getting merged into the other text.
Some examples of the blocks of text I get back are:
12324 35th Ed. 01-MAR-12 Last LNM: 14/12 NAD 83 14/12 Corrective Object of Corrective
ChartTitle: Intracoastal Waterway Sandy Hook to Little Egg Harbor Position
C HAActRionT N Y -NJ - S A N D Y H OO K ATcO tionLI T TLE EGG HARBOR. Page/Side: N/A
(Temp) indicates that the chart correction action is temporary in nature. Courses and bearings are givCGenD 0in 1 degrees clockwise from 000 true.
Bearings RoEf LlighOCtAT seEc tors aSrehre towwsbuardry th Re ivligher Ct fhroanmn seel Lawighartde.d B Theuoy 5no minal range of lights is expressedf roin mna 4u0tic-24al -mi46les.56 0(NNM ) unless othe0r7w4is-00e n-o05te.d8.8 0 W
to 40-24-48.585N 074-00-05.967W
and
12352 33rd Ed. 01-MAR-11 Last LNM: 03/12 NAD 83 04/12 . . l . . . . Corrective Object of Corrective ChartTitle: Shinnecock Bay to East Rockaway Inlet Position C HAActRionT S H IN N E C OC K B A Y TO AcEtionAS T ROCKAWAY INLET. Page/Side: N/A (Temp) indicates that the chart correction action is temporary in nature. Courses and bearings are givCGenD 0in 1 degrees clockwise from 000 true. (BTeeamringp) s DoEf LlighETtE s ectors aSretat toew Baoratd Ctheh anlighnet lf Droaym beseacoawanr 3d. The nominal range of lights is expressedf roin mna 4u0tic-37al -mi11les.52 0(NNM ) unless othe0r7w3is-29e n-5o3te.d76. 0 W
and I have discovered that the "ghost text" is ALWAYS the following:
Corrective Object of Corrective Position
Action Action
(Temp) indicates that the chart correction action is temporary in nature. Courses and bearings are given in degrees clockwise from 000 true.
Bearings of light sectors are toward the light from seaward. The nominal range of lights is expressed in nautical miles (NM) unless otherwise noted.
In the 2nd example I posted, the text I want (with the ghost text removed) is:
12352 33rd Ed. 01-Mar-11 Last LNM:03/12 NAD 83 04/12
Chart Title:Shinnecock Bay to East Rockaway Inlet. Page/Side:N/A
CGD01
(Temp) DELETE State Boat Channel Daybeacon 3 from 40-37-11.520N 073-29-53.760W
This problem occurs just once per document, and does not appear to be totally consistent (as seen above). I am wondering if one of you wizards could think of a way to remove the ghosted text (I don't need/want it) using python. If I had been using pyPDF, I would have used a regex to rip it out during the conversion to text. Unfortunately, since I'm starting out with a text file from the website listed above, the damage has already been done. I'm at a bit of a loss.
Thanks for reading.
EDIT:
The solution to this problem looks like it be more complex than the rest of the application, so I'm going to withdraw my request for help.
I very much appreciate the thought put into it by those who have contributed.

Given that the ghost text can be split up in seemingly unpredictable ways, I don't think there is a simple automatic way of removing it that would not have false positives. What you need is almost human-level pattern recognition. :-)
What you could try is exploiting the format of these kinds of messages. Roughly;
<number> <number>[rn]d Ed. <date> Last LNM:<mm>/<yy> NAD <date2>
Chart Title:<text>. Page/Side:<N/A or number(s)> CGD<number> <text>
<position>
Using this you could pluck out the nonsense from the predictable elements, and then if you have a list of chart names ('Shinnecock Bay to East Rockaway Inlet') and descriptive words (like 'State', 'Boat', 'Daybeacon') you might be able to reconstruct the original words by finding the smallest levenshtein distance between mangled words in the two text blocks and those in your word lists.
If you can install the poppler software, you could try and use pdftotext with the -layout option to keep the formatting from the original PDF as much as possible. That might make your problem disappear.

You could recursively find all possible ways that your Pattern
"Corrective Object of Corrective Position Action ..." can be contained within your mangled text,
Then you can unmangle the text for each of these possible paths, run some sort of spellcheck over them, and choose the one with the fewest spelling mistakes. Or since you know roughly where each substring should appear, you can use that as a heuristic.
Or you could simply use the first path.
some pseudocode (untested):
def findPaths(mangledText, pattern, path)
if len(pattern)==0: # end of pattern
return [path]
else:
nextLetter= pattern[0]
locations = findAllOccurences (mangledText, nextLetter) # get all indices in mangledText that contain nextLetter
allPaths = []
for loc in locations:
paths = findPaths( mangledText[loc+1:], pattern[1:], path + (loc,) )
allPaths.Extend(paths)
return allPaths # if no locations for the next letters exist, allPaths will be emtpy
Then you can call it like this (optionally remove all spaces from your search pattern, unless you are certain they are all included in the mangled text)
allPossiblePaths = findPaths ( YourMangledText, "Corrective Object...", () )
then allPossiblePaths should contain a list of all possible ways your pattern could be contained in your mangled text.
Each entry is a tuple with the same length as the pattern, containing the index at which the corresponding letter of the pattern occurs in the search text.

AttributeError: 'str' object has no attribute 'toInteger'

I'm writing a code using python to generate a point shapefile within ArcMAP. I have a 1000 random possibilities (in FileA), and I need to try all of them. The FileA is the index of the position of FileB.
In addition, for each sequence generated I'm looking at the evolution of the area of the Voronoi polygon from 3 points to 50 points in each sequence that contains a total of 50 points.
When I run the code, I have this message which confuse me:
tempXYFile.writerow('{0},{1}'.format(coordinates[entry.toInteger()][0],coordinates[entry.toInteger()][1]))
AttributeError: 'str' object has no attribute 'toInteger'
I'll appreciate any help !
This is my code:
import csv
# create 1000 XY sequences
print 'Start of the script'
sequences = csv.reader(open('FileA.csv','rb'),delimiter=',')
coordinates = []
# read coordinates of volcanos and store in memory
print 'Start reading in the coordinates into the memory'
coordinates_file = csv.reader(open('FileB.csv','rb'),delimiter=',')
for coordinate in coordinates[1:]:
coordinates.append(coordinate)
del coordinates_file
##i = 1
for sequence in sequences:
## print 'sequence # {0}'.format(i)
j = 1
tempXYFile = csv.writer(open('tempXY.csv','wb'),delimiter=',') #add the parameter to create a file if does not exist
for entry in sequence:
tempXYFile.writerow('{0},{1}'.format(coordinates[entry.toInteger()][0],coordinates[entry.toInteger()][1]))
print 'Entry # {0}: {1},{2}'.format(j, coordinates[entry.toInteger()][0],coordinates[entry.toInteger()][1])
j = j + 1
i = i + 1
del tempXYFile
print 'End of Script'

Python doesn't have a toInteger() function for strings you will want to user int(entry[]) instead.

There is no toInteger() method on strings in standard Python. The error message is pretty clear. If you want to convert a string like "37" to the integer 37, try int(entry) instead.
Why did you write toInteger() in your code?

Does not exist toInteger method on strings
Check this: http://docs.python.org/library/stdtypes.html#string-methods
The correct form is:
coordinates[int(entry)][0]