How I can overcome the _geoslib problem in this code? - matplotlib-basemap

This code is specified to visualize the CALIPSO satellite atmospheric profiles
The input files are .HDF
The code is copyrighted to the HDF group.
In the begining, I struggled with installing the basemap,
finally I installed it using .whl file on my windows10.
Now, this error is reached when I run the script:
SystemError:
execution of module _geoslib raised unreported exception.
I have looked a lot in google, but nothing done.
Can you please help me?
Cheers
"Copyright (C) 2014-2019 The HDF Group
Copyright (C) 2014 John Evans
This example code illustrates how to access and visualize a LaRC CALIPSO file
in file in Python.
If you have any questions, suggestions, or comments on this example, please use
the HDF-EOS Forum (http://hdfeos.org/forums). If you would like to see an
example of any other NASA HDF/HDF-EOS data product that is not listed in the
HDF-EOS Comprehensive Examples page (http://hdfeos.org/zoo), feel free to
contact us at eoshelp#hdfgroup.org or post it at the HDF-EOS Forum
(http://hdfeos.org/forums).
Usage: save this script and run
$python CAL_LID_L2_VFM-ValStage1-V3-02.2011-12-31T23-18-11ZD.hdf.py
The HDF file must either be in your current working directory
or in a directory specified by the environment variable HDFEOS_ZOO_DIR.
Tested under: Python 2.7.15::Anaconda custom (64-bit)
Last updated: 2019-01-25
"""
import os
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
from mpl_toolkits.basemap import Basemap
from matplotlib import colors
USE_NETCDF4 = False
def run(FILE_NAME):
# Identify the data field.
DATAFIELD_NAME = 'Feature_Classification_Flags'
if USE_NETCDF4:
from netCDF4 import Dataset
nc = Dataset(FILE_NAME)
# Subset the data to match the size of the swath geolocation fields.
# Turn off autoscaling, we'll handle that ourselves due to presence of
# a valid range.
var = nc.variables[DATAFIELD_NAME]
data = var[:,1256]
# Read geolocation datasets.
lat = nc.variables['Latitude'][:]
lon = nc.variables['Longitude'][:]
else:
from pyhdf.SD import SD, SDC
hdf = SD(FILE_NAME, SDC.READ)
# Read dataset.
data2D = hdf.select(DATAFIELD_NAME)
data = data2D[:,1256]
# Read geolocation datasets.
latitude = hdf.select('Latitude')
lat = latitude[:]
longitude = hdf.select('Longitude')
lon = longitude[:]
# Subset data. Otherwise, all points look black.
lat = lat[::10]
lon = lon[::10]
data = data[::10]
# Extract Feature Type only through bitmask.
data = data & 7
# Make a color map of fixed colors.
cmap = colors.ListedColormap(['black', 'blue', 'yellow', 'green', 'red', 'purple', 'gray', 'white'])
# The data is global, so render in a global projection.
m = Basemap(projection='cyl', resolution='l',
llcrnrlat=-90, urcrnrlat=90,
llcrnrlon=-180, urcrnrlon=180)
m.drawcoastlines(linewidth=0.5)
m.drawparallels(np.arange(-90.,90,45))
m.drawmeridians(np.arange(-180.,180,45), labels=[True,False,False,True])
x,y = m(lon, lat)
i = 0
for feature in data:
m.plot(x[i], y[i], 'o', color=cmap(feature), markersize=3)
i = i+1
long_name = 'Feature Type at Altitude = 2500m'
basename = os.path.basename(FILE_NAME)
plt.title('{0}\n{1}'.format(basename, long_name))
fig = plt.gcf()
# define the bins and normalize
bounds = np.linspace(0,8,9)
norm = mpl.colors.BoundaryNorm(bounds, cmap.N)
# create a second axes for the colorbar
ax2 = fig.add_axes([0.93, 0.2, 0.01, 0.6])
cb = mpl.colorbar.ColorbarBase(ax2, cmap=cmap, norm=norm, spacing='proportional', ticks=bounds, boundaries=bounds, format='%1i')
cb.ax.set_yticklabels(['invalid', 'clear', 'cloud', 'aerosol', 'strato', 'surface', 'subsurf', 'no signal'], fontsize=5)
# plt.show()
pngfile = "{0}.py.png".format(basename)
fig.savefig(pngfile)
if __name__ == "__main__":
# If a certain environment variable is set, look there for the input
# file, otherwise look in the current directory.
hdffile = 'CAL_LID_L2_VFM-ValStage1-V3-02.2011-12-31T23-18-11ZD.hdf'
try:
fname = os.path.join(os.environ['HDFEOS_ZOO_DIR'], ncfile)
except KeyError:
fname = hdffile
run(fname)

Please try miniconda and use basemap from conda-forge:
conda install -c conda-forge basemap

Related

i am trying to get a bokeh server to run, but when i type in the command in my terminal i get an error message

I am trying to run the code below in a bokeh server to visualize the plots. the final_imdb_dataframe is in the same directory as the python code. these are the steps i take to get the server to run:
open my terminal
type in "cd" then a space and then my directory in for the map containing my python script and the final_imdb_dataframe
press enter
type: bokeh serve --show "filename.py"
press enter
in my terminal i am getting this error message however:
bokeh : The term 'bokeh' is not recognized as the name of a cmdlet, function, script file, or operable program. (the complete error message is attached as a picture)
when i type in "pip show bokeh" in the command promt in python it gives me this:
pip show bokeh
Name: bokeh
Version: 2.4.3
Summary: Interactive plots and applications in the browser from Python
Home-page: https://github.com/bokeh/bokeh
Author: Bokeh Team
Author-email: info#bokeh.org
License: BSD-3-Clause
Location: c:\users\fazan\anaconda\lib\site-packages
Requires: Jinja2, numpy, packaging, pillow, PyYAML, tornado, typing-extensions
Required-by: hvplot, panel
Note: you may need to restart the kernel to use updated packages.
so it should work right?
i don't know what to do anymore...
code:
import pandas as pd
from bokeh.plotting import figure, show
import numpy as np
from bokeh.models import ColumnDataSource, HoverTool, Slider, RangeSlider, Div, Select
from bokeh.io import output_file, curdoc
from bokeh.layouts import column, row, layout
#EERSTE PLOT:
#line diagram of amount of movies released each year en avg rating displayed over the years
df = pd.read_csv("final_imdb_dataframe")
#"unnamed column weghalen
df.drop(df.columns[df.columns.str.contains('unnamed',case = False)],axis = 1, inplace = True)
#creating plot 2
plot2 = figure(plot_width = 1000,
plot_height = 400,
x_axis_label= "year",
title = "watchtime and movie rating over the years")
#creating a dropdown menu
source2 = ColumnDataSource(data={'x': df["release_date"], 'y': df["watchtime"]})
plot2.circle(x="x", y="y", size = 3, source = source2, alpha = 0.2)
def update_plot(attr, old, new):
if new == 'watchtime':
source2.data = {'x' : df["release_date"], 'y' : df["watchtime"]}
else:
source2.data = {'x' : df["release_date"], 'y' : df["movie_rating"]}
select = Select(title = "keuze menu", options=["watchtime", "movie_rating"], value = 'watchtime')
#code for updating the plot when the value is changed
select.on_change('value', update_plot)
#TWEEDE PLOT:
#creating a list of all the years a movie came out
dfrelease = df.release_date.drop_duplicates().tolist()
#sorting the list with release dates to get them in chronological order
dfrelease1 = sorted(dfrelease)
#creating an empty list
total_releases_per_year = []
#adding the amount of movies that came out every year to the list
for i in range(len(dfrelease1)):
total_releases_per_year.append(len(df[df["release_date"] == dfrelease1[i]]))
#creating a columndatasource of the two lists created above to make it possible for the hovertool to be used
source1 = ColumnDataSource(data=dict(year = dfrelease1, amount_of_movies_made = total_releases_per_year))
#making a hovertool
hover2 = HoverTool(tooltips=[("year", "#year"), ("amount of movies made", "#amount_of_movies_made")])
#creating plot 3
plot3 = figure(plot_width = 1000,
plot_height = 400,
x_axis_label= "year",
y_axis_label = "amount of movies",
title = "amount of movies per year")
plot3.line("year", "amount_of_movies_made", source = source1)
plot3.add_tools(hover2)
#DERDE PLOT:
#creating the ColumnDataSource
df_sel = df[df["release_date"] == 2020]
source1 = ColumnDataSource(df_sel)
#scatter plot
p1 = figure(title = "relation 'watchtime' and 'movie rating' over the years",
x_axis_label= "watchtime",
y_axis_label= "rating (0-10)",
plot_width = 1000,
plot_height = 400)
p1.circle(x="watchtime", y="movie_rating", alpha = 0.2, source=source1)
#making the rangeslider
slider = RangeSlider(title="release date", value= (1919, 2021), start=1919, end=2020, step=1)
#making the hover tool
hover1 = HoverTool(tooltips=[("title", "#movie_name"),("gross", "#gross_collection"),("votes", "#votes"),("genre", "#genre"), ("watchtime", "#watchtime"),("rating", "#movie_rating"),("release date", "#release_date")])
#making a def callback for the rangeslider to work when moved
def callback(attr, old, new):
year = slider.value
source1.data = df[(df["release_date"] >= year[0]) & (df["release_date"] <= year[1])]
slider.on_change("value", callback)
layout = column(slider, p1) #create a layout with slider on top of plot
p1.add_tools(hover1) #adding hover tool
layout3 = column(select, plot2, plot3, slider, p1) #making the layout for the dashboard
curdoc().add_root(layout3)*
i tried what i wrote above and expected acces to the bokeh server that would show me my plots. i have done this before on my previous computer (mac) and it worked then. now on my lenovo it is not working.`

How to efficiently rename many files or partially select the names of these files during import?

how to rename the files efficiently by the number in the name (see picture)? I did not succeed with Windows PowerToys and I dont wana click each file and rename to the number (e.g. 290)
or how to read the files in this order and define a name? If I try it with a script (see below) the following output occurs:
[![ValueError: invalid literal for int() with base 10: '211001_164357_P_Scripted_Powermeasurement_Wavelength_automatic_Powermeter1_0'][1]][1]
or how to select only the numbers (290 to 230 - see picture) within the name when reading?
Script:
#import libraries
import pandas as pd
import os
import matplotlib.pyplot as plt
import numpy as np
from pathlib import Path
data_location = r'C:\Users\...\Characterization_OPO\Data'
data_folder = Path(data_location)
data = {}
allist = list(data_folder.glob('*'))
for i, file in enumerate(allist):
file = str(file)
file_name = file.split('\\')[-1]
wavelength = int(file_name.split('.')[0])
tmp = pd.read_csv(file, skiprows=20, skipfooter=59, index_col="PixelNo")
data[f'{wavelength} nm'] = tmp;
#data.plot(x='Wavelength',y='CCD_1', label=f"{wavelength} nm")
Picture:
I removed all words with windows power rename and than took the last three digits:
for i, file in enumerate(allist):
file = str(file)
file_name = file.split('\\')[-1]
wavelength = int(file_name.split('.')[0])
tmp = pd.read_csv(file, skiprows=26, skipfooter=5)
data[f'{wavelength % 1000} nm'] = tmp;
#data.plot(x='Wavelength',y='CCD_1', label=f"{wavelength} nm")

ValueError: Cannot feed value of shape (1, 2048, 2048, 1) for Tensor 'image_tensor:0', which has shape '(?, ?, ?, 3)'

Using TensorFlow I am trying to detect one object(png and grayscale image). I have trained and exported a model.ckpt successfully. Now I am trying to restore the saved model.ckpt for prediction. Here is the script:
import numpy as np
import os
import six.moves.urllib as urllib
import sys
import tarfile
import tensorflow as tf
import zipfile
from collections import defaultdict
from io import StringIO
from matplotlib import pyplot as plt
from PIL import Image
if tf.__version__ != '1.4.0':
raise ImportError('Please upgrade your tensorflow installation to v1.4.0!')
# This is needed to display the images.
#matplotlib inline
# This is needed since the notebook is stored in the object_detection folder.
sys.path.append("..")
from utils import label_map_util
from utils import visualization_utils as vis_util
MODEL_NAME = 'melon_graph'
# Path to frozen detection graph. This is the actual model that is used for the object detection.
PATH_TO_CKPT = MODEL_NAME + '/frozen_inference_graph.pb'
# List of the strings that is used to add correct label for each box.
PATH_TO_LABELS = os.path.join('training', 'object_detection.pbtxt')
NUM_CLASSES = 1
detection_graph = tf.Graph()
with detection_graph.as_default():
od_graph_def = tf.GraphDef()
with tf.gfile.GFile(PATH_TO_CKPT, 'rb') as fid:
serialized_graph = fid.read()
od_graph_def.ParseFromString(serialized_graph)
tf.import_graph_def(od_graph_def, name='')
label_map = label_map_util.load_labelmap(PATH_TO_LABELS)
categories = label_map_util.convert_label_map_to_categories(label_map, max_num_classes=NUM_CLASSES, use_display_name=True)
category_index = label_map_util.create_category_index(categories)
def load_image_into_numpy_array(image):
(im_width, im_height) = image.size
return np.array(image.getdata()).reshape((im_height, im_width, 1)).astype(np.float64)
# For the sake of simplicity we will use only 2 images:
# If you want to test the code with your images, just add path to the images to the TEST_IMAGE_PATHS.
PATH_TO_TEST_IMAGES_DIR = 'test_images'
TEST_IMAGE_PATHS = [ os.path.join(PATH_TO_TEST_IMAGES_DIR, 'te_data{}.png'.format(i)) for i in range(1, 336) ]
# Size, in inches, of the output images.
IMAGE_SIZE = (12, 8)
with detection_graph.as_default():
with tf.Session(graph=detection_graph) as sess:
# Definite input and output Tensors for detection_graph
image_tensor = detection_graph.get_tensor_by_name('image_tensor:0')
# Each box represents a part of the image where a particular object was detected.
detection_boxes = detection_graph.get_tensor_by_name('detection_boxes:0')
# Each score represent how level of confidence for each of the objects.
# Score is shown on the result image, together with the class label.
detection_scores = detection_graph.get_tensor_by_name('detection_scores:0')
detection_classes = detection_graph.get_tensor_by_name('detection_classes:0')
num_detections = detection_graph.get_tensor_by_name('num_detections:0')
for image_path in TEST_IMAGE_PATHS:
image = Image.open(image_path)
# the array based representation of the image will be used later in order to prepare the
# result image with boxes and labels on it.
image_np = load_image_into_numpy_array(image)
# Expand dimensions since the model expects images to have shape: [1, None, None, 3]
image_np_expanded = np.expand_dims(image_np, axis=0)
# Actual detection.
(boxes, scores, classes, num) = sess.run([detection_boxes, detection_scores, detection_classes, num_detections], feed_dict={image_tensor: image_np_expanded})
# Visualization of the results of a detection.
vis_util.visualize_boxes_and_labels_on_image_array(image_np,np.squeeze(boxes),np.squeeze(classes).astype(np.float64), np.squeeze(scores), category_index, use_normalized_coordinates=True, line_thickness=5)
plt.figure(figsize=IMAGE_SIZE)
plt.imshow(image_np)
and this is the error
Traceback (most recent call last): File "cochlear_detection.py",
line 81, in
(boxes, scores, classes, num) = sess.run([detection_boxes, detection_scores, detection_classes, num_detections],
feed_dict={image_tensor: image_np_expanded}) File
"/anaconda/lib/python3.6/site-packages/tensorflow/python/client/session.py",
line 889, in run
run_metadata_ptr) File "/anaconda/lib/python3.6/site-packages/tensorflow/python/client/session.py",
line 1096, in _run
% (np_val.shape, subfeed_t.name, str(subfeed_t.get_shape()))) ValueError: Cannot feed value of shape (1, 2048, 2048, 1) for Tensor
'image_tensor:0', which has shape '(?, ?, ?, 3)'

Callbackfunction modelcheckpoint causes error in keras

I seem to get this error when I am using the callback function modelcheckpoint..
I read from a github issue that the solution would be make use of model.get_weight, but I am implicitly only storing that since i am only storing the one with best weight.
Keras only seem to save weights using h5, which make me question is there any other way to do store them using the eras API, if so how? If not, how do i store it?
Made an example to recreate the problem:
#!/usr/bin/python
import glob, os
import sys
from os import listdir
from os.path import isfile, join
import numpy as np
import warnings
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from keras.utils import np_utils
from keras import metrics
import keras
from keras import backend as K
from keras.models import Sequential
from keras.optimizers import SGD, Adam
from keras.layers.core import Dense, Activation, Lambda, Reshape,Flatten
from keras.layers import Conv1D,Conv2D,MaxPooling2D, MaxPooling1D, Reshape
#from keras.utils.visualize_util import plot
from keras.models import Model
from keras.layers import Input, Dense
from keras.layers.merge import Concatenate, Add
import h5py
import random
import tensorflow as tf
import math
from keras.callbacks import CSVLogger
from keras.callbacks import ModelCheckpoint
if len(sys.argv) < 5:
print "Missing Arguments!"
print "python keras_convolutional_feature_extraction.py <workspace> <totale_frames> <fbank-dim> <window-height> <batch_size>"
print "Example:"
print "python keras_convolutional_feature_extraction.py deltas 15 40 5 100"
sys.exit()
total_frames = int(sys.argv[2])
total_frames_with_deltas = total_frames*3
dim = int(sys.argv[3])
window_height = int(sys.argv[4])
inserted_batch_size = int(sys.argv[5])
stride = 1
splits = ((dim - window_height)+1)/stride
#input_train_data = "/media/carl/E2302E68302E443F/"+str(sys.argv[1])+"/fbank/org_train_total_frames_"+str(total_frames)+"_dim_"+str(dim)+"_winheig_"+str(window_height)+"_batch_"+str(inserted_batch_size)+"_fws_input"
#output_train_data ="/media/carl/E2302E68302E443F/"+str(sys.argv[1])+"/fbank/org_train_total_frames_"+str(total_frames)+"_dim_"+str(dim)+"_winheig_"+str(window_height)+"_batch_"+str(inserted_batch_size)+"_fws_output"
#input_test_data = "/media/carl/E2302E68302E443F/"+str(sys.argv[1])+"/fbank/org_test_total_frames_"+str(total_frames)+"_dim_"+str(dim)+"_winheig_"+str(window_height)+"_batch_"+str(1)+"_fws_input"
#output_test_data = "/media/carl/E2302E68302E443F/"+str(sys.argv[1])+"/fbank/org_test_total_frames_"+str(total_frames)+"_dim_"+str(dim)+"_winheig_"+str(window_height)+"_batch_"+str(1)+"_fws_output"
#train_files =[f for f in listdir(input_train_data) if isfile(join(input_train_data, f))]
#test_files =[f for f in listdir(input_test_data) if isfile(join(input_test_data, f))]
#print len(train_files)
np.random.seed(100)
print "hallo"
def train_generator():
while True:
# input = random.choice(train_files)
# h5f = h5py.File(input_train_data+'/'+input, 'r')
# train_input = h5f['train_input'][:]
# train_output = h5f['train_output'][:]
# h5f.close()
train_input = np.random.randint(100,size=((inserted_batch_size,splits*total_frames_with_deltas,window_height,3)))
train_list_list = []
train_input = train_input.reshape((inserted_batch_size,splits*total_frames_with_deltas,window_height,3))
train_input_list = np.split(train_input,splits*total_frames_with_deltas,axis=1)
for i in range(len(train_input_list)):
train_input_list[i] = train_input_list[i].reshape(inserted_batch_size,window_height,3)
#for i in range(len(train_input_list)):
# train_input_list[i] = train_input_list[i].reshape(inserted_batch_size,33,window_height,1,3)
train_output = np.random.randint(5, size = (1,total_frames,5))
middle = int(math.ceil(total_frames/2))
train_output = train_output[:,middle:middle+1,:].reshape((inserted_batch_size,1,5))
#print train_output.shape
#print len(train_input_list)
#print train_input_list[0].shape
yield (train_input_list, train_output)
print "hallo"
def test_generator():
while True:
# input = random.choice(test_files)
# h5f = h5py.File(input_test_data+'/'+input, 'r')
# test_input = h5f['test_input'][:]
# test_output = h5f['test_output'][:]
# h5f.close()
test_input = np.random.randint(100,size=((inserted_batch_size,splits*total_frames_with_deltas,window_height,3)))
test_input = test_input.reshape((inserted_batch_size,splits*total_frames_with_deltas,window_height,3))
test_input_list = np.split(test_input,splits*total_frames_with_deltas,axis=1)
#test_input_list = np.split(test_input,45,axis=3)
for i in range(len(test_input_list)):
test_input_list[i] = test_input_list[i].reshape(inserted_batch_size,window_height,3)
#for i in range(len(test_input_list)):
# test_input_list[i] = test_input_list[i].reshape(inserted_batch_size,33,window_height,1,3)
test_output = np.random.randint(5, size = (1,total_frames,5))
middle = int(math.ceil(total_frames/2))
test_output = test_output[:,middle:middle+1,:].reshape((inserted_batch_size,1,5))
yield (test_input_list, test_output)
print "hallo"
def fws():
#print "Inside"
# Params:
# batch , lr, decay , momentum, epochs
#
#Input shape: (batch_size,40,45,3)
#output shape: (1,15,50)
# number of unit in conv_feature_map = splitd
next(train_generator())
model_output = []
list_of_input = [Input(shape=(8,3)) for i in range(splits*total_frames_with_deltas)]
output = []
#Conv
skip = total_frames_with_deltas
for steps in range(total_frames_with_deltas):
conv = Conv1D(filters = 100, kernel_size = 8)
column = 0
for _ in range(splits):
#print "column " + str(column) + "steps: " + str(steps)
output.append(conv(list_of_input[(column*skip)+steps]))
column = column + 1
#print len(output)
#print splits*total_frames_with_deltas
conv = []
for section in range(splits):
column = 0
skip = splits
temp = []
for _ in range(total_frames_with_deltas):
temp.append(output[((column*skip)+section)])
column = column + 1
conv.append(Add()(temp))
#print len(conv)
output_conc = Concatenate()(conv)
#print output_conc.get_shape
output_conv = Reshape((splits, -1))(output_conc)
#print output_conv.get_shape
#Pool
pooled = MaxPooling1D(pool_size = 6, strides = 2)(output_conv)
reshape = Reshape((1,-1))(pooled)
#Fc
dense1 = Dense(units = 1024, activation = 'relu', name = "dense_1")(reshape)
#dense2 = Dense(units = 1024, activation = 'relu', name = "dense_2")(dense1)
dense3 = Dense(units = 1024, activation = 'relu', name = "dense_3")(dense1)
final = Dense(units = 5, activation = 'relu', name = "final")(dense3)
model = Model(inputs = list_of_input , outputs = final)
sgd = SGD(lr=0.1, decay=1e-1, momentum=0.9, nesterov=True)
model.compile(loss="categorical_crossentropy", optimizer=sgd , metrics = ['accuracy'])
print "compiled"
model_yaml = model.to_yaml()
with open("model.yaml", "w") as yaml_file:
yaml_file.write(model_yaml)
print "Model saved!"
log= CSVLogger('/home/carl/kaldi-trunk/dnn/experimental/yesno_cnn_50_training_total_frames_'+str(total_frames)+"_dim_"+str(dim)+"_window_height_"+str(window_height)+".csv")
filepath='yesno_cnn_50_training_total_frames_'+str(total_frames)+"_dim_"+str(dim)+"_window_height_"+str(window_height)+"weights-improvement-{epoch:02d}-{val_acc:.2f}.hdf5"
checkpoint = ModelCheckpoint(filepath, monitor='val_acc', verbose=1, save_weights_only=True, mode='max')
print "log"
#plot_model(model, to_file='model.png')
print "Fit"
hist_current = model.fit_generator(train_generator(),
steps_per_epoch=444,#len(train_files),
epochs = 10000,
verbose = 1,
validation_data = test_generator(),
validation_steps=44,#len(test_files),
pickle_safe = True,
workers = 4,
callbacks = [log,checkpoint])
fws()
Execute the script by: python name_of_script.py yens 50 40 8 1
which give me a full traceback:
full traceback
Error:
carl#ca-ThinkPad-T420s:~/Dropbox$ python mini.py yesno 50 40 8 1
Using TensorFlow backend.
Couldn't import dot_parser, loading of dot files will not be possible.
hallo
hallo
hallo
compiled
Model saved!
log
Fit
/usr/local/lib/python2.7/dist-packages/keras/backend/tensorflow_backend.py:2252: UserWarning: Expected no kwargs, you passed 1
kwargs passed to function are ignored with Tensorflow backend
warnings.warn('\n'.join(msg))
Epoch 1/10000
2017-05-26 13:01:45.851125: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use SSE4.1 instructions, but these are available on your machine and could speed up CPU computations.
2017-05-26 13:01:45.851345: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use SSE4.2 instructions, but these are available on your machine and could speed up CPU computations.
2017-05-26 13:01:45.851392: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use AVX instructions, but these are available on your machine and could speed up CPU computations.
443/444 [============================>.] - ETA: 4s - loss: 100.1266 - acc: 0.3138Epoch 00000: saving model to yesno_cnn_50_training_total_frames_50_dim_40_window_height_8weights-improvement-00-0.48.hdf5
Traceback (most recent call last):
File "mini.py", line 205, in <module>
File "mini.py", line 203, in fws
File "/usr/local/lib/python2.7/dist-packages/keras/legacy/interfaces.py", line 88, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/keras/engine/training.py", line 1933, in fit_generator
callbacks.on_epoch_end(epoch, epoch_logs)
File "/usr/local/lib/python2.7/dist-packages/keras/callbacks.py", line 77, in on_epoch_end
callback.on_epoch_end(epoch, logs)
File "/usr/local/lib/python2.7/dist-packages/keras/callbacks.py", line 411, in on_epoch_end
self.model.save_weights(filepath, overwrite=True)
File "/usr/local/lib/python2.7/dist-packages/keras/engine/topology.py", line 2503, in save_weights
save_weights_to_hdf5_group(f, self.layers)
File "/usr/local/lib/python2.7/dist-packages/keras/engine/topology.py", line 2746, in save_weights_to_hdf5_group
f.attrs['layer_names'] = [layer.name.encode('utf8') for layer in layers]
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip-4rPeHA-build/h5py/_objects.c:2684)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip-4rPeHA-build/h5py/_objects.c:2642)
File "/usr/local/lib/python2.7/dist-packages/h5py/_hl/attrs.py", line 93, in __setitem__
self.create(name, data=value, dtype=base.guess_dtype(value))
File "/usr/local/lib/python2.7/dist-packages/h5py/_hl/attrs.py", line 183, in create
attr = h5a.create(self._id, self._e(tempname), htype, space)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip-4rPeHA-build/h5py/_objects.c:2684)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip-4rPeHA-build/h5py/_objects.c:2642)
File "h5py/h5a.pyx", line 47, in h5py.h5a.create (/tmp/pip-4rPeHA-build/h5py/h5a.c:1904)
RuntimeError: Unable to create attribute (Object header message is too large)
If you look at the amount of data Keras is trying to save under layer_names attribute (inside the output HDF5 file being create), you will find that it takes more than 64kB.
np.asarray([layer.name.encode('utf8') for layer in model.layers]).nbytes
>> 77100
I quote from https://support.hdfgroup.org/HDF5/faq/limits.html:
Is there an object header limit and how does that affect HDF5 ?
There is a limit (in HDF5-1.8) of the object header, which is 64 KB.
The datatype for a dataset is stored in the object header, so there is
therefore a limit on the size of the datatype that you can have. (See
HDFFV-1089)
The code above was (almost entirely) copied from the traceback:
File "/usr/local/lib/python2.7/dist-packages/keras/engine/topology.py", line 2746, in save_weights_to_hdf5_group
f.attrs['layer_names'] = [layer.name.encode('utf8') for layer in layers]
I am using numpy asarray method to get the figure fast but h5py gets similar figure (I guess), see https://github.com/h5py/h5py/blob/master/h5py/_hl/attrs.py#L102 if you want to find exact figure.
Anyway, either you will need to implement your own methods for saving/loading of the weights (or use existing workarounds), or you need to give a really short name to ALL the layers inside your model :), something like this:
list_of_input = [Input(shape=(8,3), name=('i%x' % i)) for i in range(splits*total_frames_with_deltas)]
conv = Conv1D(filters = 100, kernel_size = 8, name='cv%x' % steps)
conv.append(Add(name='add%x' % section)(temp))
output_conc = Concatenate(name='ct')(conv)
output_conv = Reshape((splits, -1), name='rs1')(output_conc)
pooled = MaxPooling1D(pool_size = 6, strides = 2, name='pl')(output_conv)
reshape = Reshape((1,-1), name='rs2')(pooled)
dense1 = Dense(units = 1024, activation = 'relu', name = "d1")(reshape)
dense2 = Dense(units
= 1024, activation = 'relu', name = "d2")(dense1)
dense3 = Dense(units = 1024, activation = 'relu', name = "d3")(dense1)
final = Dense(units = 5, activation = 'relu', name = "fl")(dense3)
You mustn't forget to name all the layers because the (numpy) string array into which the layer names are converted is using the size of the longest string for each individual string in it when it is saved!
After renaming the layers as proposed above (which takes almost 26kB) the model is saved successfully. Hope this elaborate answer helps someone.
Update: I have just made a PR to Keras which should fix the issue without implementing any custom loading/saving methods, see 7508
A simple solution, albeit possibly not the most elegant, could be to run a while loop with epochs = 1.
Get the weights at the end of every epoch together with the accuracy and the loss
Save the weights to file 1 with model.get_weight
if accuracy is greater than at the previous epoch (i.e. loop), store the weights to a different file (file 2)
Run the loop again loading the weights from file 1
Break the loops setting a manual early stopping so that it breaks if the loss does not improve for a certain number of loops
You can use get_weights() together with numpy.save.
It's not the best solution, because it will save several files, but it actually works.
The problem is that you won't have the "optimizer" saved with the current states. But you can perhaps work around that by using smaller learning rates after loading.
Custom callback using numpy.save:
def myCallback(epoch,logs):
global storedLoss
#do your comparisons here using the "logs" var.
print(logs)
if (logs['loss'] < storedLoss):
storedLoss = logs['loss']
for i in range(len(model.layers)):
WandB = model.layers[i].get_weights()
if len (WandB) > 0: #necessary because some layers have no weights
np.save("W" + "-" + str(i), WandB[0],False)
np.save("B" + "-" + str(i), WandB[1],False)
#remember that get and set weights use a list: [weights,biases]
#it may happen (not sure) that there is no bias, and thus you may have to check it (len(WandB)==1).
The logs var brings a dictionary with named metrics, such as "loss", and "accuracy", if you used it.
You can store the losses within the callback in a global var, and compare if each loss is better or worse than the last.
When fitting, use the lambda callback:
from keras.callbacks import LambdaCallback
model.fit(...,callbacks=[LambdaCallback(on_epoch_end=myCallback)])
In the example above, I used the LambdaCallback, which has more possibilities than just on_epoch_end.
For loading, do a similar loop:
#you have to create the model first and then set the layers
def loadModel(model):
for i in range(len(model.layers)):
WandBForCheck = model.layers[i].get_weights()
if len (WandBForCheck) > 0: #necessary because some layers have no weights
W = np.load(Wfile + str(i))
B = np.load(Bfile + str(i))
model.layers[i].set_weights([W,B])
See follow-up at https://github.com/fchollet/keras/issues/6766 and https://github.com/farizrahman4u/keras-contrib/pull/90.
I saw the YAML and the root cause is probably that you have so many Inputs. A few Inputs with many dimensions is preferred to many Inputs, especially if you can use scanning and batch operations to do everything efficiently.
Now, ignoring that entirely, here is how you can save and load your model if it has too much stuff to save as JSON efficiently:
You can pass save_weights_only=True. That won't save optimizer weights, so isn't a great solution.
Just put together a PR for saving model weights and optimizer weights but not configuration. When you want to load, first instantiate and compile the model as you did when you were going to train it, then use load_all_weights to load the model and optimizer weights into that model. I'll try to merge it soon so you can use it from the master branch.
You could use it something like this:
from keras.callbacks import LambdaCallback
from keras_contrib.utils.save_load_utils import save_all_weights, load_all_weights
# do some stuff to create and compile model
# use `save_all_weights` as a callback to checkpoint your model and optimizer weights
model.fit(..., callbacks=[LambdaCallback(on_epoch_end=lambda epoch, logs: save_all_weights(model, "checkpoint-{:05d}.h5".format(epoch))])
# use `load_all_weights` to load model and optimizer weights into an existing model
# if not compiled (no `model.optimizer`), this will just load model weights
load_all_weights(model, 'checkpoint-1337.h5')
So I don't endorse the model, but if you want to get it to save and load anyways this should probably work for you.
As a side note, if you want to save weights in a different format, something like this would work.
pickle.dump([K.get_value(w) for w in model.weights], open( "save.p", "wb" ) )
Cheers
Your model architecture must be too large to be saved.
USE get_weights AND set_weights TO SAVE AND LOAD MODEL, RESPECTIVELY.
Do not use callback model checkpoint. just once the training ends, save its weights with pickle.
Have a look at this link: Unable to save DataFrame to HDF5 ("object header message is too large")

simpleITK N4BiasFieldCorrection performs strange in terms of running speed and results

I am doing a project about brain tumor segmentation. And when I apply N4BiasCorrection to my file(.mha), I used slicer and simpleITK methods.
Slicer performs well but is time-consuming because I do not know how to use code to run through all my file, I just use the Slicer-N4ITK module and process each file by hand.
Then I try the simpleITK with python, problems show up. First, it runs very slow on each .mha file and gets a really big file(36.7MB compare with 4.4MB using Slicer) after applying n4biasfieldcorrection. Second, in order to speed up, I set the Shrink parameter to 4 but the whole .mha file becomes really blurred, which will not happen using slicer.
So can anyone tell me whether it is normal ? are there any methods to speed up without blurring my file? Or could you please tell me an example to apply N4BiasFieldCorrection within Slicer python interactor .
Thanks!!
# -*- coding: utf-8 -*-
"""
Spyder Editor
This is a temporary script file.
"""
from __future__ import print_function
import SimpleITK as sitk
import sys
import os
#from skimage import io
from glob import glob
import numpy as np
def n4process(inputimage, outpath):
inputImage = sitk.ReadImage( inputimage )
# numberFilltingLevels = 4
maskImage = sitk.OtsuThreshold( inputImage, 0, 1, 200 )
# inputImage = sitk.Shrink( inputImage, [ 2 ] * inputImage.GetDimension() )
# maskImage = sitk.Shrink( maskImage, [ 2 ] * inputImage.GetDimension() )
inputImage = sitk.Cast( inputImage, sitk.sitkFloat32 )
corrector = sitk.N4BiasFieldCorrectionImageFilter();
corrector.SetConvergenceThreshold=0.001
corrector.SetBiasFieldFullWidthAtHalfMaximum=0.15
corrector.SetMaximumNumberOfIterations=50
corrector.SetNumberOfControlPoints=4
corrector.SetNumberOfHistogramBins=200
corrector.SetSplineOrder=3
corrector.SetWienerFilterNoise=0.1
output = corrector.Execute( inputImage,maskImage )
sitk.WriteImage( output, outpath )
input_path = '/Users/chenrui/Desktop/BRATS2015_Training/HGG/'
patientpath = glob('/Users/chenrui/Desktop/BRATS2015_Training/HGG/*')
num = 0
for i in patientpath:
num = num+1
#i = '/Users/chenrui/Desktop/BRATS2015_Training/HGG/brats_2013_pat0001_1'
flair = glob(i + '/*Flair*/*.mha')
flair_outpath = '/Users/chenrui/Desktop/BRATS2015_Training/test/'+'Flair/'+str(num)+'.mha'
n4process(flair[0], flair_outpath)
t2 = glob(i + '/*T2*/*.mha')
t2_outpath = '/Users/chenrui/Desktop/BRATS2015_Training/HGG_n4/'+'T2/'+str(num)+'.mha'
n4process(t2[0], t2_outpath)
t1c = glob(i + '/*_T1c*/*.mha')
t1c_outpath = '/Users/chenrui/Desktop/BRATS2015_Training/HGG_n4/'+'T1c/'+str(num)+'.mha'
n4process(t1c[0], t1c_outpath)
t1 = glob(i + '/*_T1*/*.mha')
t1 = [scan for scan in t1 if scan not in t1c]
t1_outpath = '/Users/chenrui/Desktop/BRATS2015_Training/HGG_n4/'+'T1/'+str(num)+'.mha'
n4process(t1[0],t1_outpath)
From a look at the original implementation http://www.insight-journal.org/browse/publication/640
You can download this and generate the example to then test on your data. The parameters you set appear to be the same as defined in the defaults except for WeinerFilterNoise which should be 0.01 unless you've changed this for a reason - is this the blurring issue?
The size differential (x 8 increase) will be that you've probably saved out the data from 8bit to 64 bit or something. Checking the metaimage header will show this. This can be resolved with casting.