Plotting Data with Basemap - mask

I am trying to plot the following dataset using a Basemap instance:
[-0.126929 -0.127279 -0.127851 ..., -0.14199 -0.142828 -0.14335 ]
The problem is I can't have the right number of points displayed on the map. (which is the length of my data list above = 1315 points).
If I define my dataset to be like:
data = np.diag(data)
[[-0.126929 0. 0. ..., 0. 0. 0. ]
[ 0. -0.127279 0. ..., 0. 0. 0. ]
[ 0. 0. -0.127851 ..., 0. 0. 0. ]
...,
[ 0. 0. 0. ..., -0.14199 0. 0. ]
[ 0. 0. 0. ..., 0. -0.142828 0. ]
[ 0. 0. 0. ..., 0. 0. -0.14335 ]]
I have this figure
If I define my dataset to be like:
data = np.ma.masked_where(data==0., data)
[[-0.12692899999999696 -- -- ..., -- -- --]
[-- -0.12727900000000147 -- ..., -- -- --]
[-- -- -0.12785099999999971 ..., -- -- --]
...,
[-- -- -- ..., -0.14198999999999984 -- --]
[-- -- -- ..., -- -0.1428280000000015 --]
[-- -- -- ..., -- -- -0.1433499999999981]]
I have this figure
fig = plt.figure()
m = Basemap(projection='mill', \
llcrnrlon= lonmin-0.02, \
urcrnrlon= lonmax+0.02, \
llcrnrlat= latmin-0.02, \
urcrnrlat= latmax+0.02, \
resolution='f')
cmap = plt.cm.get_cmap('bwr_r')
x, y = m(*np.meshgrid(lon,lat))
y = y.T
cs = m.contourf(x,y,data,cmap=cmap)
m.drawcoastlines(linewidth=1.,color='grey')
m.drawcountries(linewidth=1.5,color='white')
m.drawmapboundary(color='k',linewidth=2.0)
m.fillcontinents(color='white')
cb = m.colorbar(cs,location='bottom',size='5%',pad='8%')
cb.set_label('[m]',fontsize=12)
plt.show()

Related

TypeError: Caught TypeError in DataLoader worker process 0. TypeError: 'KeyError' object is not iterable

from torchvision_starter.engine import train_one_epoch, evaluate
from torchvision_starter import utils
import multiprocessing
import time
n_cpu = multiprocessing.cpu_count()
device = torch.device('cuda') if torch.cuda.is_available() else torch.device('cpu')
_ = model.to(device)
params = [p for p in model.parameters() if p.requires_grad]
optimizer = torch.optim.Adam(model.parameters(), lr=0.00001)
lr_scheduler = torch.optim.lr_scheduler.StepLR(optimizer,
step_size=3,
gamma=0.2,
verbose=True
)
# Let's train for 10 epochs
num_epochs = 1
start = time.time()
for epoch in range(10, 10 + num_epochs):
# train for one epoch, printing every 10 iterations
train_one_epoch(model, optimizer, data_loaders['train'], device, epoch, print_freq=10)
# update the learning rate
lr_scheduler.step()
# evaluate on the validation dataset
evaluate(model, data_loaders['valid'], device=device)
stop = time.time()
print(f"\n\n{num_epochs} epochs in {stop - start} s ({(stop-start) / 3600:.2f} hrs)")
Before I move on to this part, everything is OK. But after I run the part, the error is like below:
I have tried to add drop_last to the helper.py's function like:
data_loaders["train"] = torch.utils.data.DataLoader(
train_data,
batch_size=batch_size,
sampler=train_sampler,
num_workers=num_workers,
collate_fn=utils.collate_fn,
drop_last=True
)
But it doesn't work. By the way, the torch and torchvision are compatible and Cuda is available.
I wonder how to fix it.
The get_data_loaders function:
def get_data_loaders(
folder, batch_size: int = 2, valid_size: float = 0.2, num_workers: int = -1, limit: int = -1, thinning: int = None
):
"""
Create and returns the train_one_epoch, validation and test data loaders.
:param foder: folder containing the dataset
:param batch_size: size of the mini-batches
:param valid_size: fraction of the dataset to use for validation. For example 0.2
means that 20% of the dataset will be used for validation
:param num_workers: number of workers to use in the data loaders. Use -1 to mean
"use all my cores"
:param limit: maximum number of data points to consider
:param thinning: take every n-th frame, instead of all frames
:return a dictionary with 3 keys: 'train_one_epoch', 'valid' and 'test' containing respectively the
train_one_epoch, validation and test data loaders
"""
if num_workers == -1:
# Use all cores
num_workers = multiprocessing.cpu_count()
# We will fill this up later
data_loaders = {"train": None, "valid": None, "test": None}
# create 3 sets of data transforms: one for the training dataset,
# containing data augmentation, one for the validation dataset
# (without data augmentation) and one for the test set (again
# without augmentation)
data_transforms = {
"train": get_transform(UdacitySelfDrivingDataset.mean, UdacitySelfDrivingDataset.std, train=True),
"valid": get_transform(UdacitySelfDrivingDataset.mean, UdacitySelfDrivingDataset.std, train=False),
"test": get_transform(UdacitySelfDrivingDataset.mean, UdacitySelfDrivingDataset.std, train=False),
}
# Create train and validation datasets
train_data = UdacitySelfDrivingDataset(
folder,
transform=data_transforms["train"],
train=True,
thinning=thinning
)
# The validation dataset is a split from the train_one_epoch dataset, so we read
# from the same folder, but we apply the transforms for validation
valid_data = UdacitySelfDrivingDataset(
folder,
transform=data_transforms["valid"],
train=True,
thinning=thinning
)
# obtain training indices that will be used for validation
n_tot = len(train_data)
indices = torch.randperm(n_tot)
# If requested, limit the number of data points to consider
if limit > 0:
indices = indices[:limit]
n_tot = limit
split = int(math.ceil(valid_size * n_tot))
train_idx, valid_idx = indices[split:], indices[:split]
# define samplers for obtaining training and validation batches
train_sampler = torch.utils.data.SubsetRandomSampler(train_idx)
valid_sampler = torch.utils.data.SubsetRandomSampler(valid_idx) # =
# prepare data loaders
data_loaders["train"] = torch.utils.data.DataLoader(
train_data,
batch_size=batch_size,
sampler=train_sampler,
num_workers=num_workers,
collate_fn=utils.collate_fn,
drop_last=True
)
data_loaders["valid"] = torch.utils.data.DataLoader(
valid_data, # -
batch_size=batch_size, # -
sampler=valid_sampler, # -
num_workers=num_workers, # -
collate_fn=utils.collate_fn,
drop_last=True
)
# Now create the test data loader
test_data = UdacitySelfDrivingDataset(
folder,
transform=data_transforms["test"],
train=False,
thinning=thinning
)
if limit > 0:
indices = torch.arange(limit)
test_sampler = torch.utils.data.SubsetRandomSampler(indices)
else:
test_sampler = None
data_loaders["test"] = torch.utils.data.DataLoader(
test_data,
batch_size=batch_size,
shuffle=False,
num_workers=num_workers,
sampler=test_sampler,
collate_fn=utils.collate_fn,
drop_last=True
# -
)
return data_loaders
class UdacitySelfDrivingDataset(torch.utils.data.Dataset):
# Mean and std of the dataset to be used in nn.Normalize
mean = torch.tensor([0.3680, 0.3788, 0.3892])
std = torch.tensor([0.2902, 0.3069, 0.3242])
def __init__(self, root, transform, train=True, thinning=None):
super().__init__()
self.root = os.path.abspath(os.path.expandvars(os.path.expanduser(root)))
self.transform = transform
# load datasets
if train:
self.df = pd.read_csv(os.path.join(self.root, "labels_train.csv"))
else:
self.df = pd.read_csv(os.path.join(self.root, "labels_test.csv"))
# Index by file id (i.e., a sequence of the same length as the number of images)
codes, uniques = pd.factorize(self.df['frame'])
if thinning:
# Take every n-th rows. This makes sense because the images are
# frames of videos from the car, so we are essentially reducing
# the frame rate
thinned = uniques[::thinning]
idx = self.df['frame'].isin(thinned)
print(f"Keeping {thinned.shape[0]} of {uniques.shape[0]} images")
print(f"Keeping {idx.sum()} objects out of {self.df.shape[0]}")
self.df = self.df[idx].reset_index(drop=True)
# Recompute codes
codes, uniques = pd.factorize(self.df['frame'])
self.n_images = len(uniques)
self.df['image_id'] = codes
self.df.set_index("image_id", inplace=True)
self.classes = ['car', 'truck', 'pedestrian', 'bicyclist', 'light']
self.colors = ['cyan', 'blue', 'red', 'purple', 'orange']
#property
def n_classes(self):
return len(self.classes)
def __getitem__(self, idx):
if idx in self.df.index:
row = self.df.loc[[idx]]
else:
return KeyError(f"Element {idx} not in dataframe")
# load images fromm file
img_path = os.path.join(self.root, "images", row['frame'].iloc[0])
img = Image.open(img_path).convert("RGB")
# Exclude bogus boxes with 0 height or width
h = row['ymax'] - row['ymin']
w = row['xmax'] - row['xmin']
filter_idx = (h > 0) & (w > 0)
row = row[filter_idx]
# get bounding box coordinates for each mask
boxes = row[['xmin', 'ymin', 'xmax', 'ymax']].values
# convert everything into a torch.Tensor
boxes = torch.as_tensor(boxes, dtype=torch.float32)
# get the labels
labels = torch.as_tensor(row['class_id'].values, dtype=int)
image_id = torch.tensor([idx])
area = (boxes[:, 3] - boxes[:, 1]) * (boxes[:, 2] - boxes[:, 0])
# assume no crowd for everything
iscrowd = torch.zeros((row.shape[0],), dtype=torch.int64)
target = {}
target["boxes"] = boxes
target["labels"] = labels
target["image_id"] = image_id
target["area"] = area
target["iscrowd"] = iscrowd
if self.transform is not None:
img, target = self.transform(img, target)
return img, target
def __len__(self):
return self.n_images
def plot(self, idx, renormalize=True, predictions=None, threshold=0.5, ax=None):
image, label_js = self[idx]
if renormalize:
# Invert the T.Normalize transform
unnormalize = T.Compose(
[
T.Normalize(mean = [ 0., 0., 0. ], std = 1 / type(self).std),
T.Normalize(mean = -type(self).mean, std = [ 1., 1., 1. ])
]
)
image, label_js = unnormalize(image, label_js)
if ax is None:
fig, ax = plt.subplots(figsize=(8, 8))
_ = ax.imshow(torch.permute(image, [1, 2, 0]))
for i, box in enumerate(label_js['boxes']):
xy = (box[0], box[1])
h, w = (box[2] - box[0]), (box[3] - box[1])
r = patches.Rectangle(xy, h, w, fill=False, color=self.colors[label_js['labels'][i]-1], lw=2, alpha=0.5)
ax.add_patch(r)
if predictions is not None:
# Make sure the predictions are on the CPU
for k in predictions:
predictions[k] = predictions[k].detach().cpu().numpy()
for i, box in enumerate(predictions['boxes']):
if predictions['scores'][i] > threshold:
xy = (box[0], box[1])
h, w = (box[2] - box[0]), (box[3] - box[1])
r = patches.Rectangle(xy, h, w, fill=False, color=self.colors[predictions['labels'][i]-1], lw=2, linestyle=':')
ax.add_patch(r)
_ = ax.axis("off")
return ax

IDL two step graph

I'm struggling with setting a y(x) condition that varies with x range. As an example below, the code wants to plot y=x between x=0 and x=5.1; otherwise y=2x.
Upon compilation, the code spits out the following: Expression must be a scalar or 1 element array in this context:
In other words don't know how to assign an array variable 'x' into if statement.
Thank you all for your help in advance.
PRO test
x = findgen(101.0,start=0)/10.0 ; 0.0 start, 10.0 end increment of 0.1
print,x
if x lt 5.1 then begin
y = 1.0 * x ;
endif else begin
y = 2.0* x
endelse
graph1=plot(x,y,thick=2,NAME=first,/CURRENT, $
linestyle = 0, ytitle=' y',xtitle='x' ) ; O
END
The problem is the test in your IF statement. Use WHERE instead to do something like the following.
y = x ;; need to initialize variable
low = WHERE(x lt 5.1,lw,COMPLEMENT=upp,NCOMPLEMENT=up)
IF (lw[0] GT 0) THEN y[low] = x[low] ;; technically don't need this line
IF (up[0] GT 0) THEN y[upp] = 2e0*x[upp]

Standard ML: Size of binary tree computed incorrectly?

My book has the following function which calculates the number of non-leaf nodes in a binary tree:
fun size Empty = 0
| size(Node(t_1, _, t_2)) = size t_1 + size t_2 + 1;
Suppose I want to calculate all nodes in a binary tree. How would I modify this function to do so?
Here's what I was thinking:
fun size Empty = 0
| size(Node(Empty, _, Empty)) = 1
| size(Node(t_1, _, t_2)) = size t_1 + size t_2 + 1;
Does this look right?
Thanks,
bclayman
Both of the implementations that you provided are actually the same. The second case of your second implementation is a special case of you your third pattern. For your first implementation, size(Node(Empty,1,Empty)) will recurse one the left subtree, returning 0, recurse on the right subtree, which returns 0, and then adds 1, yielding the result 1. In fact, if you switch the order of the second and third case, the compiler will tell you that it is redundant:
test.sml:3.5-5.38 Error: match redundant
Empty => ...
Node (t_1,_,t_2) => ...
--> Node (Empty,_,Empty) => ...
Matt is correct that your two functions are functionally the same -- both of which return a count of all nodes in the tree. I didn't notice this at first since I took it at face value that your first function counted nonleaf nodes and then noticed that your Node(Empty,_,Empty) pattern is the correct pattern of a leaf (if a leaf is defined as a node with no non-empty children). But -- this means that the function in the book doesn't just count nonleaf (parents) nodes. If you do want a function which just counts parent nodes, there is a use for your pattern after all:
fun parents Empty = 0
| parents(Node(Empty, _, Empty)) = 0
| parents(Node(t_1, _, t_2)) = parents t_1 + parents t_2 + 1;
If your application of trees is one in which heavy use is made of the parent node vs. leaf node distinction, you could (at the cost of making some of your function definitions more involved) ditch the Node constructor in favor of separate Parent and Leaf constructors. Something like:
datatype 'a tree = Empty | Leaf of 'a | Parent of 'a tree * 'a * 'a tree;
Then you can write functions like
fun countLeaves Empty = 0
| countLeaves (Leaf _) = 1
| countLeaves (Parent(t1,_,t2)) = countLeaves t1 + countLeaves t2;
So e.g.
- val t = Parent(Parent(Leaf "2", "*", Leaf "3"), "+", Leaf "4");
- countLeaves t;
val it = 3 : int

Issue with recursion not hitting base case

I'm working on the following DCG:
zero(1) -->
[0],
!.
zero(N) -->
{
N < 1
},
[],
!.
zero(N) -->
zero(1),
{
M is N - 1
},
zero(M).
It works properly for positive test cases, eg
?- phrase(zero(5), A).
A = [0, 0, 0, 0, 0].
?- phrase(zero(2), [0,0]).
true.
But when I ran negative cases (typically something like phrase(zero(5), [0,0]).), it goes into oblivian. Curiously, during tracing, it seems whenever it goes to the zero(1) line in the third clause during recursion, it doesn't go to the basecase (first clause), instead jumps to the second one and fails because N = 1. Any guesses?
I think your problem is over-specified, and you don't want the cuts. In particular, you don't need the "negative" case:
zero(N) -->
{
N < 1
},
[],
!.
This will SUCCEED on what you consider to be a failure case.
Instead, try something a little simpler:
zero(1) --> [0].
zero(N) --> { N > 1, M is N - 1 }, [0], zero(M).
This defines only the positive cases. All other cases fail. So:
| ?- phrase(zero(5), A).
A = [0,0,0,0,0]
yes
| ?- phrase(zero(2), [0,0]).
yes
| ?- phrase(zero(5), [0,0]).
no
| ?-

Making turtles wait x number of ticks

Part of what I am trying to do is make a breed of turtles move around, but when one reaches its destination that turtle waits for a certain number of ticks before continuing ? Also is it possible to make turtles wait for different number of ticks depending upon their destination ( different patch colors). Is it a case of making a turtle breed or global variable to count the number of ticks? The hopefully relevant code is below.
You are right, this can be done by making the turtles count the number of ticks they have been on a patch. Also this has to be a turtle variable and not a global variable since each turtle will have a different value for this
The approach, I have used is this:
Once the turtle arrives at its destination record the ticks (the global variable which records the number of ticks that have passed till now) into a turtle variable say ticks-since-here. This works like a time-stamp.
On each successive tick check the difference between the current-time ticks global variable and the ticks-since-here turtle variable. If this becomes greater than the number of ticks the turtle is allowed to stay on the patch, let it choose and move to the new destination.
breed [visitors visitor]
globals [ number-of-visitors ]
visitors-own [
; visitors own destination
destination
ticks-since-here
]
to go
ask visitors [
move
]
tick
end
to move
; Instructions to move the agents around the environment go here
; comparing patch standing on to dest, if at dest then choose random new dest
; then more forward towards new dest
ifelse ( patch-here = destination )
[
if ticks - ticks-since-here > ticks-to-stay-on-patch patch-here
[
set ticks-since-here 0
set destination one-of patches with
[
pcolor = 65 or pcolor = 95 or pcolor = 125 or pcolor = 25 or pcolor = 15 or pcolor = 5
]
]
]
[
face destination
forward 1
if ( patch-here = destination )
[
set ticks-since-here ticks
]
]
end
to-report ticks-to-stay-on-patch [p]
if [pcolor] of p = 65
[
report 6
]
if [pcolor] of p = 95
[
report 5
]
if [pcolor] of p = 125
[
report 4
]
if [pcolor] of p = 25
[
report 3
]
if [pcolor] of p = 15
[
report 2
]
if [pcolor] of p = 5
[
report 1
]
end
to setup-people
;;;; added the following lines to facilitate world view creation
ask patches
[
set pcolor one-of [65 95 125 25 15 5]
]
set number-of-visitors 100
;;;;
create-visitors number-of-visitors
[
ask visitors
[
; set the shape of the visitor to "visitor"
set shape "person"
; set the color of visitor to white
set color white
; give person a random xy
setxy (random 50) (random 50)
; set visitors destination variable
set destination one-of patches with
[
pcolor = 65 or pcolor = 95 or pcolor = 125 or pcolor = 25 or pcolor = 15 or pcolor = 5
]
]
]
end

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