I've been recently trying to use rpy2 and import zoo library into python.
however, when I run the following sets of code, I receive the following error
from rpy2.robjects.packages import importr
r_zoo = importr("zoo")
r_zoo.rollapply(ddf,FUN = r_func.fun1, width = 10, align = "left",by_column = True)
res = super(Function, self).call(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in FUN(data[posns], ...) : unused
argument (by_column = TRUE)
The equivalent r code is
rollapply(ddf,FUN = r_func.fun1, width = 10, align = "left",by.column = True)
I understand that when we use the importr from rpy2.robjects.packages it automatically converts the '.' in Rlang to '_' in python.
Two ways to get around that problem:
Use a kwargs dict
r_zoo.rollapply(ddf,FUN = r_func.fun1, width = 10, align = "left",**{"by.column":True})
Explicitly specify that by_column is to be translated to by.column
from rpy2.robjects.functions import SignatureTranslatedFunction`
r_zoo.rollapply = SignatureTranslatedFunction(r_zoo.rollapply, init_prm_translate = {'by_column': 'by.column'})
Source
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I am trying to do Catia V5 automation using python. I managed to create my baseline sketch without any problem however, I am unable to set axis for volumic operations. Here is a simple example that (should) create a round ball by revolving around the global Z axis :
import os
from win32com.client import Dispatch
CATIA = Dispatch('CATIA.Application')
CATIA.Visible = True
from pathlib import Path
# Creating the part and the sketch
partDocument1 = CATIA.Documents.Add("Part")
part1 = partDocument1.Part
bodies1 = part1.Bodies
body1 = bodies1.Item("PartBody")
sketches1 = body1.Sketches
originElements1 = part1.OriginElements
reference1 = originElements1.PlaneYZ
sketch1 = sketches1.Add(reference1)
# Creating the baseline sketch
sketch1.OpenEdition()
geometricElements1 = sketch1.GeometricElements
axis2D1 = geometricElements1.Item("AbsoluteAxis")
circle2D1 = sketch1.Factory2D.CreateCircle(0.000000, 0.000000, 100, 1.570796, 4.712389)
# Volumic operation
shapeFactory1 = part1.ShapeFactory
reference8 = part1.CreateReferenceFromName("")
shaft1 = shapeFactory1.AddNewShaftFromRef(reference8)
reference9 = part1.CreateReferenceFromObject(sketch1)
shaft1.SetProfileElement(reference9)
hybridShapes1 = body1.HybridShapes
hybridShapeLineExplicit1 = hybridShapes1.Item("Z Axis")
reference10 = part1.CreateReferenceFromObject(hybridShapeLineExplicit1)
shaft1.RevoluteAxis = reference10
part1.UpdateObject(shaft1)
part1.Update()
And here is the traceback :
hybridShapeLineExplicit1 = hybridShapes1.Item("Z Axis")
File "<COMObject <unknown>>", line 2, in Item
I think my problem comes from the fact that this axis is located "outside" the sketch used for the shaft. I dont know how to define an axis in this python "vba-like" code.
Could you help me ?
Thank you very much !
I am trying to run DESeq2 through rpy2 for the first time and am having some difficulties.
class py_DESeq2:
def __init__(self, count_matrix):
self.dds = None
self.normalized_count_matrix = None
self.vsd = None
self.count_matrix = robjects.conversion.py2rpy(count_matrix)
self.design_matrix = robjects.conversion.py2rpy(pd.DataFrame({'treatment':['ctrl' for i in range(count_matrix.shape[1])]}))
self.design_formula = Formula('~ 1')
def norm_counts(self, **kwargs):
self.dds = deseq.DESeqDataSetFromMatrix(countData=self.count_matrix, colData=self.design_matrix, design=self.design_formula)
self.vsd = deseq.varianceStabilizingTransformation(self.dds, blind=True)
self.normed_count_matrix = deseq.assay(self.vsd)
self.normed_count_matrix = to_dataframe(self.normed_count_matrix)
self.normed_count_matrix = robjects.conversion.rpy2py(self.normed_count_matrix)
I get the following error at self.normed_count_matrix = deseq.assay(self.vsd):
module 'DESeq2' has no attribute 'assay'
The below code in R runs fine:
library(DESeq2)
countData <- read.delim("0.333404867983521.R.data.in.txt")
colData <- read.delim("0.333404867983521.R.groups.in.txt")
dds <- DESeqDataSetFromMatrix(countData, colData,design=~Treatment,tidy=TRUE)
norm <- varianceStabilizingTransformation(dds,blind=TRUE)
norm_matrix <- assay(norm)
norm_df <- data.frame(Gene=rownames(norm_matrix), norm_matrix)
write.table(norm_df, "0.333404867983521.R.data.out.txt", row.names = FALSE,sep="\t")
The norm object is a <class 'rpy2.robjects.methods.RS4'>.
There must be something I am missing here and a point in the right direction would be appreciated!
If you open R and type:
library(DESeq2)
assay
you will see that the assay function is not actually coming from DESeq2, but from its dependency which is called SummarizedExperiment:
> assay
standardGeneric for "assay" defined from package "SummarizedExperiment"
function (x, i, withDimnames = TRUE, ...)
standardGeneric("assay")
<bytecode: 0x5586a354db90>
<environment: 0x5586a3535e20>
Methods may be defined for arguments: x, i
Use showMethods("assay") for currently available ones.
you can confirm that assay is not part of DESeq2 by using explicit namespaces in R:
> DESeq2::assay
Error: 'assay' is not an exported object from 'namespace:DESeq2'
and to confirm that it is indeed a part of SummarizedExperiment:
> SummarizedExperiment::assay
standardGeneric for "assay" defined from package "SummarizedExperiment"
Therefore in rpy2 you can use it like this:
from rpy2.robjects.packages import importr
summarized_experiment = importr('SummarizedExperiment')
summarized_experiment.assay(self.vsd)
I am getting an error when trying to use my custom fastai dataset
The error:
Exception: Can't infer the type of your targets.
It's either because your data source is empty or because your labeling function raised an error.
The code:
from fastai import *
from fastai.vision import *
class URL:
MURDERHORNETS = f"https://superdata.quinniboi10.repl.co/MurderHornetImages"
path = untar_data(URL.MURDERHORNETS)
'''
path = untar_data(URLs.PETS)
files = get_image_files(path)
import PIL
img = PIL.Image.open(files[0])
img
'''
fnames = get_image_files(path)
fnames[:5]
np.random.seed (2)
pat = r'/([^/]+)_\d+\.(png|jpg|jpeg)$'
data = ImageDataBunch.from_folder(path, train=path, test=None, valid_pct=0.2,
ds_tfms=get_transforms(),
size=160)
data.normalize (imagenet_stats)
data.show_batch(rows=3, figsize=(7,6))
print (data.classes)
len (data.classes),data.c
learn = cnn_learner(data, models.resnet50, metrics=error_rate)
learn.fit_one_cycle(5)
learn.save ('stage-1')
The dataset is here, don't comment on the name, I don't know why that is what I chose :/
Get the zip file of the dataset here
I want to add rows to a datagridview "manually". I tried converting the following code to python: https://learn.microsoft.com/en-us/dotnet/framework/winforms/controls/how-to-manipulate-rows-in-the-windows-forms-datagridview-control
However, I struggle with adding rows. The following doesn't work:
for j in range(len(signals)):
self._dataGridView1.Rows.Add(signals[j])
The following code does work, but is not dynamically enough as I don't know how many elements there will be:
for j in range(len(signals)):
self._dataGridView1.Rows.Add(signals[j][0], signals[j][1], signals[j][2], signals[j][3])
How should I fix this? I tried tuple, but the result were a tuple with all the info shown in the first cell instead of spread over the columns.
I would not like to add packages, as this is to be run within revid dynamo among several users, and I cannot convince everyone to install packages.
full code for context:
import clr
clr.AddReference('System.Windows.Forms')
clr.AddReference('System.Drawing')
clr.AddReference('System.Data')
clr.AddReference('RevitAPIUI')
from Autodesk.Revit.UI import TaskDialog
from System.Windows.Forms import *
from System.Drawing import (
Point, Size,
Font, FontStyle,
GraphicsUnit
)
from System.Data import DataSet
from System.Data.Odbc import OdbcConnection, OdbcDataAdapter
msgBox = TaskDialog
headers = IN[0]
signals = IN[1]
class DataGridViewQueryForm(Form):
def __init__(self):
self.Text = 'Signals'
self.ClientSize = Size(942, 255)
self.MinimumSize = Size(500, 200)
self.setupDataGridView()
def setupDataGridView(self):
self._dataGridView1 = DataGridView()
self._dataGridView1.AllowUserToOrderColumns = True
self._dataGridView1.ColumnHeadersHeightSizeMode = DataGridViewColumnHeadersHeightSizeMode.AutoSize
self._dataGridView1.Dock = DockStyle.Fill
self._dataGridView1.Location = Point(0, 111)
self._dataGridView1.Size = Size(506, 273)
self._dataGridView1.TabIndex = 3
self._dataGridView1.ColumnCount = len(headers)
self._dataGridView1.ColumnHeadersVisible = True
for i in range(len(headers)):
self._dataGridView1.Columns[i].Name = headers[i]
for j in range(len(signals)):
self._dataGridView1.Rows.Add(signals[j][0], signals[j][1], signals[j][2], signals[j][3])
self.Controls.Add(self._dataGridView1)
Application.Run(DataGridViewQueryForm())
Figured it out. Had to use System.Array.
from System import Array
code changes:
array_str = Array.CreateInstance(str, len(headers))
for j in range(len(signals)):
for k in range(len(headers)):
array_str[k] = signals[j][k]
self._dataGridView1.Rows.Add(array_str)
I have a function called analyze() which is like following:
def analyze():
for stmt in irsb.statements:
if isinstance(stmt, pyvex.IRStmt.WrTmp):
wrtmp(stmt)
if isinstance(stmt, pyvex.IRStmt.Store):
address = stmt.addr
address1 = '{}'.format(address)[1:]
print address1
data = stmt.data
data1 = '{}'.format(data)[1:]
tmp3 = store64(address1, int64(data1))
if isinstance(stmt, pyvex.IRStmt.Put):
expr = stmt.expressions[0]
putoffset = stmt.offset
data = stmt.data
data4 = '{}'.format(data)[1:]
if (str(data).startswith("0x")):
#const_1 = ir.Constant(int64, data4)
tmp = put64(putoffset, ZERO_TAG)
else:
put64(putoffset, int64(data4))
if isinstance(stmt.data, pyvex.IRExpr.Const):
reg_name = irsb.arch.translate_register_name(stmt.offset, stmt.data.result_size(stmt.data.tag))
print reg_name
stmt.pp()
This code function gets following input and try to analyze it:
CODE = b"\xc1\xe0\x05"
irsb = pyvex.block.IRSB(CODE, 0x80482f0, archinfo.ArchAMD64())
When this input is in the same file in my code (lets call the whole as analyze.py) it works and python analyze.py will make me an output. However, I want to make a seperate file(call array.py), call analyze there and also put the inputs inside it and run python array.py to get the same result. I did the following for array.py:
from analyze import analyze
CODE = b"\xc1\xe0\x05"
irsb = pyvex.block.IRSB(CODE, 0x80482f0, archinfo.ArchAMD64())
analyze()
However, when I run the array.py, it stops me with error;
NameError: name 'CODE' is not defined
how can I resolve this problem? What is the solution?
A simple change in your function, add parameters:
def analyze(irsb): # irsb here called parameter
...
# The rest is the same
And then pass arguments when calling it:
from analyze import analyze
CODE = b"\xc1\xe0\x05"
irsb_as_arg = pyvex.block.IRSB(CODE, 0x80482f0, archinfo.ArchAMD64())
analyze(irsb_as_arg) # irsb_as_arg is an argument
I have just changed here irsb to irsb_as_arg to take attention, but it can be the same name