I want to modify the position of atoms that fulfil a specific condition.
Currently, I can apply translation to all atoms or one atom but not multiple selected atoms.
from pyiron import Project
pr = Project('test')
uc = pr.create_ase_bulk('Fe',cubic=True)
uc.set_repeat(2)
shift = [.1,.2,.3]
uc.positions
For example, I want to translate only atoms whose Z coordinate is less than 1:
uc[uc.positions[:,2] < 1].positions += shift
uc.positions
Neither it moves atoms nor it returns any error.
However, translating only one atom or all atoms are working properly.
uc.positions += shift
uc.positions
uc[0].position += shift
uc[0]
This one should work:
uc.positions[uc.positions[:,2] < 1] += shift
In principle when you are working with positions, cell etc., it's always safer to use the setter/getter of the attributes (and not the setter/getter of Atoms). I personally use the setter of Atoms only to change atom species, e.g. uc[0] = 'Ni'.
Related
I've followed "Procedural Generation in Godot: Dungeon Generation" by KidsCanCode #https://www.youtube.com/watch?v=o3fwlk1NI-w and find myself unable to debug the current problem.
This specific commit has the code, but I'll try to explain in more detail bellow.
My main scene has a Camera2D node, a generic Node2D calles Rooms and a TileMap, everything is empty.
When the script starts, it runs a
func make_room(_pos, _size):
position = _pos
size = _size
var s = RectangleShape2D.new()
s.custom_solver_bias = 0.5
s.extents = size
$CollisionShape2D.shape = s
A few times and it fills $Rooms using .add_child(r) where r is a instance of the node that has the make_room() function. It will then iterate over $Rooms.get_children() a few times to create a AStar node to link all the rooms:
The magic comes when make_map() is called after afterwards, it fills the map with non-walkable blocks and then it carves the empty spaces, which works fine too:
There is a find_start_room() that is called to find the initial room, it also sets a global variable to the Main script start_room, which is used to write 'Start' on the map using draw_string(font, start_room.position - Vector2(125,0),"start",Color(3,4,8))
When I hit 'esc' it runs this simple code to instance the player:
player = Player.instance()
add_child(player)
player.position = start_room.position + Vector2(start_room.size.x/2, start_room.size.y/2)
play_mode = true
The problem comes when spawning the player. I tried doing some 'blind' fixing, such as adding or subtracting a Vector2(start_room.size.x/2, start_room.size.y/2) to player.position to see if I could make it fall within the room, to no avail.
Turning to the debugger didn't help, as the positions expressed by the variable inspectors don't seem to mean anything.
I tried implementing a simple 'mouse click print location':
print("Mouse Click/Unclick at: ", event.position)
print("Node thing",get_node("/root/Main/TileMap").world_to_map(event.position))
And also a 'start_room' print location:
print(get_node("/root/Main/TileMap").world_to_map(start_room.position))
And a when player moves print location, written directly into the Character script:
print(get_node("/root/Main/TileMap").world_to_map(self.position))
Getting results like the ones bellow:
Mouse Click/Unclick at: (518, 293)
Node thing(16, 9)
(-142, 0)
(-147, -3)
So, the player doesn't spawn on the same position as the start_room and the mouse position information is not the same as anything else.
Why is the player now spawning correctly? How can I debug this situation?
EDIT1: User Theraot mentioned about how the RigidBody2D is doing some weird collisions, and from what I understood, changing their collision behavior should fix the whole thing.
There's a section on the code that -after generating the random rooms- it removes some of the rooms like this:
for room in $Rooms.get_children():
if randf() < cull:
room.queue_free()
else:
room.mode = RigidBody2D.MODE_STATIC
room_positions.append(Vector3(room.position.x, room.position.y, 0))
From what I understand, if the room is randomly selected it will be deleted using queue_free() OR it will be appended to a room_positions for further processing. This means if I shift all the rooms to a different collision layer, the player/character instance would be alone with the TileMap on the same collision layer.
So I just added a simple room.collision_layer = 3 changing this section of the code to
for room in $Rooms.get_children():
if randf() < cull:
room.queue_free()
else:
room.mode = RigidBody2D.MODE_STATIC
room.collision_layer = 3
room_positions.append(Vector3(room.position.x, room.position.y, 0))
It doesn't seem to have changed anything, the player still spawns outside the room.
Do you see the rooms spread outwards?
You didn't write code to move the rooms. Sure, the code gives them a random position. But even if you set their position to Vector2.ZERO they move outwards, avoiding overlaps.
Why? Because these rooms are RigidBody2D, and they do push other physics objects. Such as other rooms or the player character.
That's the problem: These rooms are RigidBody2D, and you put your KinematicBody2D player character on top of one of them. The RigidBody2D pushes it out.
The tutorial you followed is exploiting this behavior of RigidBody2Ds to spread the rooms. However you don't need these RigidBody2D after you are done populating your TileMap.
Instead, you can store the start position in a variable for later placing the player character (you don't need offsets - by the way - the position of the room is the center of the room), and then remove the RigidBody2Ds. If you want to keep the code that writes the text, you would also have to modify it, so it does not fail when the room no longer exists.
Alternatively, you can edit their collision layer and mask so they don't collide with the player character (or anything for that matter, but why would you want these RigidBody2Ds that collide with nothing?).
Addendum post edit: Collision layers and mask don't work as you expect.
First of all, the collision layer and mask are flags. The values of the layers are powers of two (1, 2, 4, 8...). So, when you set it to 3, it is the layer 1 plus the layer 2. So it still collides with a collision mask of 1.
And second, even if you changed the collision layer of the rooms to 2 (so it does not match the collision mask of 1 that the player character has). The player character still has a layer 1 which match the collision mask of the rooms.
See also the proposal Make physics layers and masks logic simple and consistent.
Thus, you would need to change the layer and mask. Both. in such way that they don't collide. For example, you can set layer and mask to 0 (which disable all collisions). The algorithm that populates the TileMap does not use the layer and mask.
I'm making a script that sorts the depth for my objects by prioritizing the y variable, but then afterwards checks to see if the objects that are touching each other have a higher depth the further to the right they are, but for some reason the last part isn't working.
Here's the code:
ds_grid_sort(_dg,1,true);
_yy = 0;
repeat _inst_num
{
_inst = _dg[# 0, _yy];
with _inst
{
with other
{
if (x > _inst.x and y = _inst.y)
{
_inst.depth = depth + building_space;
}
}
}
_yy++;
}
I've identified that the problem is that nothing comes out as true when the game checks the y = _inst.y part of the _inst statement, but that doesn't make any sense seeing how they're all at the same y coordinate. Could someone please tell me what I'm doing wrong?
As Steven mentioned, it's good practice to use double equal signs for comparisons (y == _inst.y) and a single equals sign for assignments (_yy = 0;), but GML doesn't care if you use a single equals sign for comparison, so it won't be causing your issue. Though it does matter in pretty much every other language besides GML.
From what I understand, the issue seems to be your use of other. When you use the code with other, it doesn't iterate through all other objects, it only grabs one instance. You can test this by running this code and seeing how many debug messages it shows:
...
with other
{
show_debug_message("X: "+string(x)+"; Y: "+string(y));
...
You could use with all. That will iterate through all objects or with object, where object is either an object or parent object. That will iterate through all instances of that object. However, neither of these functions check whether the objects overlap (it's just going to iterate over all of them), so you'll have to check for collisions. You could do something like this:
...
with all
{
if place_meeting(x, y, other)
{
if (x > _inst.x and y = _inst.y)
{
_inst.depth = depth + building_space;
}
}
...
I don't know what the rest of your code looks like, but there might be an easier way to achieve your goal. Is it possible to initially set the depth based on both the x and y variables? Something such as depth = -x-y;? For people not as familiar with GameMaker, objects with a smaller depth value are drawn above objects with higher depth values; that is why I propose setting the depth to be -x-y. Below is what a view of that grid would look like (first row and column are x and y variables; the other numbers would be the depth of an object at that position):
Having one equation that everything operates on will also make it so that if you have anything moving (such as a player), you can easily and efficiently update their depth to be able to display them correctly relative to all the other objects.
I think it should be y == _inst.y.
But I'm not sure as GML tends to accept such formatting.
It's a better practise to use == to check if they're equal when using conditions.
I am seeking a solution of connecting all the lines that have the same slope and share a common point. For example, after I load a STL file and cut it using a plane, the cutter output includes the points defining the contour. Connecting them one by one forms a (or multiple) polyline. However, some lines can be merged when their slopes are the same and they share a common point. E.g., [[0,0,0],[0,0,1]] and [[0,0,1],[0,0,2]] can be represented by one single line [[0,0,0],[0,0,2]].
I wrote a function that can analyse all the lines and connect them if they can be merged. But when the number of lines are huge, this process is slow. I am thinking in the VTK pipeline, is there a way to do the line merging?
Cheers!
plane = vtk.vtkPlane()
plane.SetOrigin([0,0,5])
plane.SetNormal([0,0,1])
cutter = vtk.vtkCutter()
cutter.SetCutFunction(plane)
cutter.SetInput(triangleFilter.GetOutput())
cutter.Update()
cutStrips = vtk.vtkStripper()
cutStrips.SetInputConnection(cutter.GetOutputPort())
cutStrips.Update()
cleanDataFilter = vtk.vtkCleanPolyData()
cleanDataFilter.AddInput(cutStrips.GetOutput())
cleanDataFilter.Update()
cleanData = cleanDataFilter.GetOutput()
print cleanData.GetPoint(0)
print cleanData.GetPoint(1)
print cleanData.GetPoint(2)
print cleanData.GetPoint(3)
print cleanData.GetPoint(4)
The output is:
(0.0, 0.0, 5.0)
(5.0, 0.0, 5.0)
(10.0, 0.0, 5.0)
(10.0, 5.0, 5.0)
(10.0, 10.0, 5.0)
Connect the above points one by one will form a polyline representing the cut result. As we can see, the line [point0, point1] and [point1, point2] can be merged.
Below is the code for merging the lines:
Assume that the LINES are represented by list: [[(p0),(p1)],[(p1),(p2)],[(p2),(p3)],...]
appended = 0
CurrentLine = LINES[0]
CurrentConnectedLine = CurrentLine
tempLineCollection = LINES[1:len(LINES)]
while True:
for HL in tempLineCollection:
QCoreApplication.processEvents()
if checkParallelAndConnect(CurrentConnectedLine, HL):
appended = 1
LINES.remove(HL)
CurrentConnectedLine = ConnectLines(CurrentConnectedLine, HL)
processedPool.append(CurrentConnectedLine)
if len(tempLineCollection) == 1:
processedPool.append(tempLineCollection[0])
LINES.remove(CurrentLine)
if len(LINES) >= 2:
CurrentLine = LINES[0]
CurrentConnectedLine = CurrentLine
tempLineCollection = LINES[1:len(LINES)]
appended = 0
else:
break
Solution:
I figured out a way of further accelerating this process using some vtk data structure. I found out that a polyline line will be stored in a cell, which can be checked by using GetCellType(). Since the point order for a polyline is sorted already, We do not need to search globally which lines are colinear with the current one. For each point on the polyline, I just need to check the point[i-1], point[i], point[i+1]. And if they are colinear, the end of the line will be updated to the next point. This process continues until the end of the polyline is reached. The speed increases by a huge amount compared with the global search approach.
Not sure if it is the main source of slowness (depends on how many positive hits on the colinearity you have), but removing items from a vector is costly (O(n)), since it requires reorganizing the rest of the vector, you should avoid it. But even without hits on colinearity, the LINES.remove(CurrentLine) call is surely slowing things down and there isn't really any need for it - just leave the vector untouched, write the final results to a new vector (processedPool) and get rid of the LINES vector in the end. You can modify your algorithm by making a bool array (vector), initialized at "false" for each item, then when you remove a line, you don't actually remove it, but only mark it as "true" and you skip all lines for which you have "true", i.e. something like this (I don't speak python so the syntax is not accurate):
wasRemoved = bool vector of the size of LINES initialized at false for each entry
for CurrentLineIndex = 0; CurrentLineIndex < sizeof(LINES); CurrentLineIndex++
if (wasRemoved[CurrentLineIndex])
continue // skip a segment that was already removed
CurrentConnectedLine = LINES[CurrentLineIndex]
for HLIndex = CurrentLineIndex + 1; HLIndex < sizeof(LINES); HLIndex++:
if (wasRemoved[HLIndex])
continue;
HL = LINES[HLIndex]
QCoreApplication.processEvents()
if checkParallelAndConnect(CurrentConnectedLine, HL):
wasRemoved[HLIndex] = true
CurrentConnectedLine = ConnectLines(CurrentConnectedLine, HL)
processedPool.append(CurrentConnectedLine)
wasRemoved[CurrentLineIndex] = true // this is technically not needed since you won't go back in the vector anyway
LINES = processedPool
BTW, the really correct data structure for LINES to use for that kind of algorithm would be a linked list, since then you would have O(1) complexity for removal and you wouldn't need the boolean array. But a quick googling showed that that's not how lists are implemented in Python, also don't know if it would not interfere with other parts of your program. Alternatively, using a set might make it faster (though I would expect times similar to my "bool array" solution), see python 2.7 set and list remove time complexity
If this does not do the trick, I suggest you measure times of individual parts of the program to find the bottleneck.
I am just curious on how do I determine whether a simplified boolean expression is in a SOP form or POS form.
for example this question:
Question
the answer to this expression is : NOT B.D/ ⌝B.D
and this is in SOP form
Can anyone explain why?
I think this should be a 'philosophical' argument. ⌝B.D is the special case where the number of elements to be summed up becomes one.
You can think of ⌝B.D = ⌝B.D + ⌝B.B + ⌝D.D + 0.(anything) which makes it an SOP.
Terminology:
First the theory, you can further study on Wikipedia (DNF, CNF):
Sum of products = DNF (Disjunctive normal form) = disjunction (+) of conjunctions (·) ~ "the disjunction is not inside any bracket, but only
as the root operator(s)".
Product of sums = CNF (Conjunctive normal form) = conjuction of disjunctions ~ "the conjunction is not inside a bracket, but only
as the root operator(s)".
Full/Complete CNF/DNF = the terms (products/sums) contains all given variables in either direct or negated form; the terms are then maxterms/minterms.
Finding the right circles:
You can see, that the four circles in the Karnaugh map correspond to the four products in the original function in the same order (top to bottom, left to right).
Given function as a SOP:
The function is now in a form of sum of products, because you can literally see, that there are four products.
It is also in the form of sum of maxterms, because the four parts contain all variables in their direct or negated form.
f(a,b,c,d) = ¬a·¬b·¬c·d + ¬a·¬b·c·d + a·¬b·c·d + a·¬b·¬c·d
For example the first term: ¬a·¬b·¬c·d ~ if the variables a, b and c are logical zeros and only d is true, then the function's output is logical 1.
Minimized function as a SOP:
You can see, that the maxterms can be grouped and that creates the minimal sum of product: f(a,b,c,d) = ¬b·d, because all cells, where b is a logical 0 and d is a logical 1 are included.
The minimized function is indeed a SOP/DNF, because it certainly does contain only one product — the ¬b·d — and there is no + (disjunction) operator inside that product.
Minimized function as a POS:
The surprise might come when you realize, that circling and writing the function as a product of sums yields the same minimal form: f(a,b,c,d) = (¬b)·(d), because there are exactly two terms: ¬b (orange circle) and d (red circle).
Both are sums with only one operand. Because of that the minimized function is a product of sum.
Conclusion:
The minimized function f(a,b,c,d) = ¬b·d is both a SOP and a POS. You can check the correct solution by using wolframalpha.com.
I need to develop an application where a user (physiotherapist) will perform a movement in front of the Kinect, I'll write the data movement in the database and then the patient will try to imitate this motion. The system will calculate the similarity between the movement recorded and executed.
My first idea is, during recording (each 5 second, by example), to store the position (x, y, z) of the points and then compare them in the execution time(by patient).
I know that this approach is too simple, because I imagine that in people of different sizes the skeleton is recognized differently, so the comparison is not reliable.
My question is about the best way to compare a saved motion with a movement executed (on the fly).
I have done this, where a doctors frame is projected onto the patients frame, but with the whole skeleton this doesn't work so well because of different bone heights :/. The code can be found here. It is in beta 2 code, the more current version can be found here, although it is not currently working perfectly
As for comparing, do something like this
for (int i = 0; i < patientList.Count; i++)
{
int diff = (int)Math.Abs(patientList[i] - doctorList[i]);
if (diff < 100) //or whatever number you want
{
Debug.WriteLine("Good Job");
}
}
I have abandoned the idea of a whole figure because of the bone heights mentioned by Fixus, so my current program looks some thing like:
EDIT
This is the concept of camparing two movements with kinect and calculate a similarity between the two movements I explain in depth.
Suppose I have the following 2 points, point A (0, 0, 0) and point B (1, 1, 1). Now I want to find the difference from point A to B, so I would subtract all of the X, Y, and Z numbers, so the difference is 1 X 1 Y 1 Z. That is the simple stuff. Now to implement it. The code I have written above, I would implement like this.
//get patient hand coordinates
double patienthandX = Canvas.GetLeft(patienthand);
double patienthandY = Canvas.GetTop(patienthand);
//get doctor hand coordinates
double doctorhandX = Canvas.GetLeft(doctorhand);
double doctorhandY = Canvas.GetTop(doctorhand);
//compare difference for each x and y
//take Absolute value so that it is positive
double diffhandX = Math.Abs(patienthandX - doctorhandX);
double diffhandY = Math.Abs(patienthandY - doctorhandY);
Now here comes another issue. The doctor coordinates are always the same, but what if the patient isn't standing where the doctor coordinates were recorded? Now we implement more simple math. Take this simple example. suppose I want point A(8, 2) to move to point B(4, 12). You multiply the x and y's of A to get to B. So I would multiply the X by .5, and the Y by 6. So for Kinect, I would put a element on the patients hip, then compare this to the doctors hip. Then multiply all of the doctor joints by that number to achieve the doctor joints on top of the patients (more or less). For example
double whatToMultiplyX = (double) doctorhipX / patienthipX;
double whatToMultiplyY = (double) doctorhipY / patienthipY;
This is all pretty simple, but bringing it together is the harder part. So far we, 1) Scale the doctor frames on top of the patient frames, 2) Calculate the difference. 3) Compare the difference throughout the entire rep. and 4) Reset for the next rep. This seems simple but it is not. To calculate the entire difference for the rep, do something like this:
//get patient hand coordinates
double patienthandX = Canvas.GetLeft(patienthand);
double patienthandY = Canvas.GetTop(patienthand);
//get doctor hand coordinates
double doctorhandX = Canvas.GetLeft(doctorhand);
double doctorhandY = Canvas.GetTop(doctorhand);
//compare difference for each x and y
//take Absolute value so that it is positive
double diffhandX = Math.Abs(patienthandX - doctorhandX);
double diffhandY = Math.Abs(patienthandY - doctrorhandY);
//+= so that it keeps adding to it.
totaldiffhandX += diffhandX;
totaldiffhandY += diffhandY;
Now we can compare, and say:
if (totaldiffhandX < 1000 && totaldiffhandY < 1000) //keep numbers pretty high since it is an entire rep
{
//reset difference
totaldiffhandX = 0;
totaldiffhandY = 0;
//tell the patient good job
Debug.WriteLine("Good Job");
}
This is pretty easy, but keep in mind you must do this for every single joint's x and y. Otherwise it will not work. Hope this Helps.
First of all remember that people are diffrent. Every person has diffrent height, width, weight, diffrent bones length etc etc
You`re code probably will never work cause of this.
Secondly you need to think more geometrically. Don`t think about points only, think with vectors, their directions. Each movement is movent of some vectors in some directions.
Then the proportion. You need to configure application for each user.
You have some pattern. The patter is your physiotherapist. You need to remember not only his movements but also his body. Arm length, leg length, distances etc. Each user that will be using your app also need to me mesured. Having all this data you can compare movement by scaling sizes and comparing directions of movent
Of course remember that there are some very simple moves like for example. They can be recognized by simple mathematic by checking actual position of the hand and checking direction of the movement. You need for this 3 control points and you`re at home :)
Gesture recognizing isn`t a simple thing