Try to find the code with function to set/change the slice label for a line plot in DM script, but could not find it.
I mean the codes could change the label "slice 1" to "ages" in a line plot with DM script.
The command you seek is ImageDisplaySetSliceLabelByID and the example how to use it is:
image img := RealImage("Slice Demo",4,100,3)
img.ShowImage()
img = icol*(irow+random())
imageDisplay disp = img.ImageGetImageDisplay(0)
disp.ImageDisplayChangeDisplayType(3)
disp.LinePlotImageDisplaySetLegendShown(1)
OKDialog("Now rename slices")
number nSlices = disp.LinePlotImageDisplayCountSlices()
for( number i=0; i<nSlices; i++ )
{
object id = disp.ImageDisplayGetSliceIDByIndex( i )
disp.ImageDisplaySetSliceLabelByID( id, "entry #"+(i+1) )
}
The examples section on Lineplot-displays in the F1 help is generally a good starting point for these things:
Related
I wrote a script to convert the EELS map to EELS line scan data, and it works well with DM 2.0. I can deal with it as directly collected EELS line scan data with DM2.0. But it does not work with DM 3.0 and the above version. It looks DM 3.0 still recognizes it as an EELS map file. DM3.0 still tried to generate elemental maps with multiple windows from it not generate line scan profiles with one single window and said the display type is incorrect. Not sure what code/command I need to add to fit the DM 3.0 and above versions. Appreciate any suggestions/comments.
image source
source := getFrontImage()
number sizeX,sizeY,sizeZ
source.Get3Dsize(sizeX,sizeY,sizeZ)
Result( "Original size:"+ sizeX +"; "+ sizeY+"; "+sizeZ+""+"\n" )
image sum
number regionsizeX = 1
number regionsizeY = sizeY
number row,col
Result( "new size:"+ regionsizeX +"; "+ regionsizeY+"; "+row+""+row+" "+"\n" )
sum := RealImage("Line Scan of [0,0,"+regionSizeY+","+regionSizeX+"]",4,sizeX/regionSizeX,sizey/regionsizeY,sizeZ)
//sum := ImageClone(source)
sum = 0
for (row=0;row<regionsizeY;row++) for (col=0;col<regionSizeX;col++)
{
OpenAndSetProgressWindow("Doing sub-block","x = "+col," y = "+row)
sum += Slice3(source,col,row,0,0,sizeX/regionSizeX,regionsizeX,1,sizeY/regionSizeY,regionSizeY,2,sizez,1)
}
OpenAndSetProgressWindow("","","")
ImageCopyCalibrationFrom(sum, source)
sum.setdisplaytype (1)
sum.SetStringNote( "Meta Data:Format", "Spectrum image" )
sum.SetStringNote( "Meta Data:Signal", "EELS" )
showimage(sum)
I'm also a bit confused by your terminology. When you write "Convert a Map into a LineScan" do you mean:
a) Convert a 3D Spectrum-Image (xy scan, one spectral dimension) into a 2D Line-Scan Spectrum-Image (one spatial dimension, one spectral dimension)
or
b) Convert a 2D Map (xy scan, one value) in a 1D Line-Trace (one spatial dimension, one value per point) ?
I suppose you mean a) and answer to that.
I'm surprised if/that your script would work without issues in GMS 2.
Your final (supposedly line-scan SI) data is still a 3D dataset with the dispersion running in Z-direction. This is not the typical LineScan SI data format (which is dispersion in X, spatial dimension in Y, no Z dimension).
Am I right in thinking that you want to "collapse" your 3D data along the y-dimension (by summing) ?
If so, what you want to do is:
// Get Input
image src3D := GetFrontImage()
number sizeX,sizeY,sizeZ
if ( 3 != src3D.ImageGetNumDimensions() ) Throw( "Input not 3D")
src3D.Get3Dsize(sizeX,sizeY,sizeZ)
// Optional: Use Rect-ROI on image to specify area
// If no selection, will return full FOV
number t,l,b,r
src3D.GetSelection(t,l,b,r)
// Prepare output (for summing 3D of rect-selection along y)
// NB: 2D container has:
// X dimension (spatial) along Y
// Z dimension (energy) along X
number nSpatial = r - l
number nSpectral = sizeZ
number eOrig, eScale, sOrig, sScale
string eUnit, sUnit
src3D.ImageGetDimensionCalibration(0, sOrig, sScale, sUnit, 0)
src3D.ImageGetDimensionCalibration(2, eOrig, eScale, eUnit, 0)
string name
if ( nSpatial != sizeX )
name = "Y-projection of [" + t + "," + l + "," + b + "," + r + "] over " + (b-t) + " rows"
else
name = "Y-projection over " + sizeY + " rows"
image dst2D := RealImage( name, 4, nSpectral, nSpatial )
dst2D.ImageSetDimensionCalibration(0, eOrig, eScale, eUnit, 0)
dst2D.ImageSetDimensionCalibration(1, sOrig, sScale, sUnit, 0)
// Copy Tags (contains necessary meta tags! Meta Data Format & Signal)
dst2D.ImageGetTagGroup().TagGroupCopyTagsFrom( src3D.ImageGetTagGroup() )
// Display (with captions)
dst2D.ShowImage()
dst2D.ImageGetImageDisplay(0).ImageDisplaySetCaptionOn(1)
number doFAST = 0
if ( !doFAST )
{
// Perform actuall summing (projection) by summing "line by line"
// into the LinePlot SI. Note the flipping of input and output dimensions!
for( number y = t; y<b; y++ )
{
number lineNumber = y - t
dst2D.slice2( 0,0,0, 0,nSpectral,1, 1,nSpatial,1 ) += src3D.slice2( l,y,0, 2,nSpectral,1, 0,nSpatial,1)
}
}
else
{
// Alternative (faster) projection. Use dedicated projection command.
image proj := src3D[l,t,0,r,b,nSpectral].Project(1) // Outcome of projectsion is having x=x and y=z, so need flip axis
dst2D = proj.slice2(0,0,0, 1,nSpectral,1, 0,nSpatial,1 ) // Flip axis
}
// Display (with captions)
dst2D.ShowImage()
dst2D.ImageGetImageDisplay(0).ImageDisplaySetCaptionOn(1)
Note that iterating using slice blocks is fast, but not as fast as the dedicated 'Project' command available in latest GMS versions. The example uses either, but lines #51-56 might not be available in older GMS.
Edit to address comment below:
Other relevant meta data for spectra is also found in the tags. For EELS, in particular the collection & convergence angle as well as the HT is of importance. You can find out about the tag-path by checking the tags of a properly acquired EELS spectrum.
Or, you can find out about their tag-paths by "converting" an empty 1D line-plot into an EELS spectrum and then attempting a quantification. You will get the prompt to fill in the data. After doing so, check the tags of the image:
I have a set of points and I want to create line / road network from those points. Firstly, I need to determine the closest point from each of the points. For that, I used the KD Tree and developed a code like this:
def closestPoint(source, X = None, Y = None):
df = pd.DataFrame(source).copy(deep = True) #Ensure source is a dataframe, working on a copy to keep the datasource
if(X is None and Y is None):
raise ValueError ("Please specify coordinate")
elif(not X in df.keys() and not Y in df.keys()):
raise ValueError ("X and/or Y is/are not in column names")
else:
df["coord"] = tuple(zip(df[X],df[Y])) #create a coordinate
if (df["coord"].duplicated):
uniq = df.drop_duplicates("coord")["coord"]
uniqval = list(uniq.get_values())
dupl = df[df["coord"].duplicated()]["coord"]
duplval = list(dupl.get_values())
for kq,vq in uniq.items():
clstu = spatial.KDTree(uniqval).query(vq, k = 3)[1]
df.at[kq,"coord"] = [vq,uniqval[clstu[1]]]
if([uniqval[clstu[1]],vq] in list(df["coord"]) ):
df.at[kq,"coord"] = [vq,uniqval[clstu[2]]]
for kd,vd in dupl.items():
clstd = spatial.KDTree(duplval).query(vd,k = 1)[1]
df.at[kd,"coord"] = [vd,duplval[clstd]]
else:
val = df["coord"].get_values()
for k,v in df["coord"].items():
clst = spatial.KDTree(val).query(vd, k = 3)[1]
df.at[k,"coord"] = [v,val[clst[1]]]
if([val[clst[1]],v] in list (df["coord"])):
df.at[k,"coord"] = [v,val[clst[2]]]
return df["coord"]
The code can return the the closest points around. However, I need to ensure that no double lines are created (e.g (x,y) to (x1,y1) and (x1,y1) to (x,y)) and also I need to ensure that each point can only be used as a starting point of a line and an end point of a line despite the point being the closest one to the other points.
Below is the visualization of the result:
Result of the code
What I want:
What I want
I've also tried to separate the origin and target coordinate and do it like this:
df["coord"] = tuple(zip(df[X],df[Y])) #create a coordinate
df["target"] = "" #create a column for target points
count = 2 # create a count iteration
if (df["coord"].duplicated):
uniq = df.drop_duplicates("coord")["coord"]
uniqval = list(uniq.get_values())
for kq,vq in uniq.items():
clstu = spatial.KDTree(uniqval).query(vq, k = count)[1]
while not vq in (list(df["target"]) and list(df["coord"])):
clstu = spatial.KDTree(uniqval).query(vq, k = count)[1]
df.set_value(kq, "target", uniqval[clstu[count-1]])
else:
count += 1
clstu = spatial.KDTree(uniqval).query(vq, k = count)[1]
df.set_value(kq, "target", uniqval[clstu[count-1]])
but this return an error
IndexError: list index out of range
Can anyone help me with this? Many thanks!
Answering now about the global strategy, here is what I would do (rough pseudo-algorithm):
current_point = one starting point in uniqval
while (uniqval not empty)
construct KDTree from uniqval and use it for next line
next_point = point in uniqval closest to current_point
record next_point as target for current_point
remove current_point from uniqval
current_point = next_point
What you will obtain is a linear graph joining all your points, using closest neighbors "in some way". I don't know if it will fit your needs. You would also obtain a linear graph by taking next_point at random...
It is hard to comment on your global strategy without further detail about the kind of road network your want to obtain. So let me just comment your specific code and explain why the "out of range" error happens. I hope this can help.
First, are you aware that (list_a and list_b) will return list_a if it is empty, else list_b? Second, isn't the condition (vq in list(df["coord"]) always True? If yes, then your while loop is just always executing the else statement, and at the last iteration of the for loop, (count-1) will be greater than the total number of (unique) points. Hence your KDTree query does not return enough points and clstu[count-1] is out of range.
I want to resize my text in plot_net but none of the options are working for me. I am trying
p <- plot_net(physeqP, maxdist = 0.4, point_label = "ID", color = "Cond", shape = "Timeperiod") p + geom_text(size=15)
This gives me error
"Error: geom_text requires the following missing aesthetics: x, y,
label".
Can anyone please tell me how can I fix the issue?
I dont want to resize legends or the axis, but the nodes text.
this image is drawn using phyloseq but since the font size is very small, i want to make it prominent.
Without an example it's hard to reproduce.
p <- plot_net(physeqP, maxdist = 0.4, point_label = "ID"
, color = "Cond", shape = "Timeperiod", cex_val = 2)
I believe this is with the NeuralNetTools package.
Try using: cex_val numeric value indicating size of text labels, default 1
https://www.rdocumentation.org/packages/NeuralNetTools/versions/1.5.0/topics/plotnet
I want to get some subarea of an image and make it a new image, and then execute further functions on it.
How can I use mouse to select a subarea of an image?
I know img[] could get the subarea of img, but I need some function by which I can interact with img. I mean, I want to get a WYSIWYG effect.
Is there any commands available, or is there any methods of ROI capable?
There different ways to do what you want in a script: You could ask the user to place an ROI and then use the [] to address this area. If you want to get a new image from this selection (CTRL + C and CTRL + SHIFT + V without scripting) you would write:
ShowImage( ImageClone( img[] ) )orimg[].ImageClone().ShowImage()
If you want to place a ROI for the user, you can used SetSelection() for a simple, rectangle, volatile ROI, or you use the full ROI commands like in this example:
image img := RealImage( "Test", 4, 256, 256 ) // create image
img.ShowImage() // show the image (so that it has a display)
imageDisplay disp = img.ImageGetImageDisplay(0) // Get the 'display' of an image
ROI myR = NewRoi() // create ROI
myR.ROISetRectangle( 110, 120, 130, 140 ) // Make it a rectangle of given area
myR.ROISetVolatile( 0 ) // make it non-volatile
myR.ROISetLabel( "Selection" ) // give it a label
myR.ROISetColor( 0, 1, 0 ) // make it green
disp.ImageDisplayAddROI( myR ) // add it to the display
A full list of ROI commands can be found in the following section of the F1 help documentation:
For my Python class were using turtle graphics.
We have too draw a target that appears at a random location on the screen. Got that.
Then a pop up window appears asking for what you think the coordinates of the target are. First the pop up box asks you to enter the x coordinate then it asks you to enter the y coordinate.
I'm having trouble saving the users inputed integers from my Tkinter window into variables I can use later in the program.
from Tkinter import *
window = Tk()
window.title("Player Input")
window.geometry('+350+130')
thexinput = IntVar()
L1 = Label(window, text="Enter the x coordinate for Mike")
L1.pack( side = LEFT)
E1= Entry(window, textvariable= thexinput, bd =5)
E1.pack(side = RIGHT)
def userinput():
global inp
a = raw_input(thexinput.get())
inp = a
b = Button(window, text = 'Submit', command = userinput)
b.pack(side = BOTTOM)
window.mainloop()
You don't need to use raw_input, you just need to call the get method of the entry widget.
a = thexinput.get()