DataFlow appears to be stuck. - on reading images from Google Storage - tensorflow

I have a DataFlow job, which first reads in 2 text files, located in Google Cloud Storage. The text files contain the paths to images also located in Google Cloud Storage.
After some inspections, I can confirm that reading the text files is successful, but the DataFlow job is stuck at reading the images. The same code runs perfectly locally. Which makes me think that maybe the image paths are incorrect, but it's not.
Here's my job ID: 2018-01-10_12_16_56-8294573519126715750
Any advice would be appreciated. Also any pointers on how to solve / debug this problem would be really useful as I don't even know where to start.
Thanks
Pipeline Definition
def configure_pipeline(pipeline, args):
read_input_source = beam.io.ReadFromText(args.input_path, strip_trailing_newlines=True)
read_img_paths = beam.io.ReadFromText(args.input_imgs, strip_trailing_newlines=True)
img_paths = (pipeline | 'Read image paths' >> read_img_paths)
train_points = (pipeline | 'Read data point' >> read_input_source)
_ = (train_points | "Read image" >> beam.ParDo(ExtractDataDoFn(), beam.pvalue.AsIter(img_paths)))
Read Images - Most of the code is simply parsing the image paths from the text file and some data to index the image.
class ExtractDataDoFn(beam.DoFn):
def start_bundle(self, context=None):
# Each frame has its own path to its image
self.frame_number_to_name = {}
def process(self, element, img_paths):
try:
line = element.element
except AttributeError:
pass
if not self.frame_number_to_name:
for path in img_paths:
if len(path) > 4:
frame_number = int(path[-10 : -4])
self.frame_number_to_name[frame_number] = path
line_tokens = element.split(':')
pivot_example = line_tokens[0].strip('\'')
example = line_tokens[1].strip('\'')
label = int(line_tokens[2])
# Get image paths
pivot_frame_number = int(pivot_example.split(',')[0])
pivot_path = self.frame_number_to_name[pivot_frame_number]
example_frame_number = int(example.split(',')[0])
example_path = self.frame_number_to_name[example_frame_number]
# Read images
def _open_file_read_binary(uri):
try:
return file_io.FileIO(uri, mode='rb')
except errors.InvalidArgumentError:
return file_io.FileIO(uri, mode='r')
# Read pivot
try:
with _open_file_read_binary(pivot_path) as f:
pivot_image_bytes = f.read()
pivot_img = Image.open(io.BytesIO(pivot_image_bytes)).convert('RGB')
except Exception as e: # pylint: disable=broad-except
logging.exception('Error processing image %s: %s', pivot_example, str(e))
return
# Read example
try:
with _open_file_read_binary(example_path) as f:
example_image_bytes = f.read()
example_img = Image.open(io.BytesIO(example_image_bytes)).convert('RGB')
except Exception as e: # pylint: disable=broad-except
logging.exception('Error processing image %s: %s', example, str(e))
return
# Convert to Numpy array
pivot_np = np.array(pivot_img)
example_np = np.array(example_img)
def _get_feature(line, img):
frame_number = int(line.split(',')[0])
y, x = int(line.split(',')[3]), int(line.split(',')[2])
h, w = int(line.split(',')[5]), int(line.split(',')[4])
bb = img[y : y + h, x : x + w, :]
return bb
# Get raw content of bounding box
pivot_feature = _get_feature(pivot_example, pivot_np)
example_feature = _get_feature(example, example_np)
# Resize data
pivot_feature = Image.fromarray(pivot_feature).resize((224, 224))
example_feature = Image.fromarray(example_feature).resize((224, 224))
# Convert back to numpy
pivot_feature = np.array(pivot_feature, np.float64)
example_feature = np.array(example_feature, np.float64)
# print(pivot_feature.shape)
yield pivot_feature, example_feature, label

Related

Why wont the NASA pictures display?

The pictures are not displaying. The code executes just fine. I took out the api key.
def gimmePictures(num):
for n in range(0,num):
now = datetime.datetime.now()
day4Pictures= now - datetime.timedelta(days = n)
data = {'api_key':'',
'date':day4Pictures.date()}
print(data)
# using the paramas argument in our request
result = requests.get('https://api.nasa.gov/planetary/apod',params=data)
# create a dictionary for yesterday's picture
dict_day = result.json()
print(dict_day['date'])
Image(dict_day['url'])
gimmePictures(10)
How can I display an image from a file in Jupyter Notebook?
def gimmePictures(num):
listofImageNames=[]
for n in range(0,num):
now = datetime.datetime.now()
day4Pictures= now - datetime.timedelta(days = n)
data = {'api_key':'dcS6cZ9DJ4zt9oXwjF6hgemj38bNJo0IGcvFGZZj', 'date':day4Pictures.date()}
# using the paramas argument in our request
result = requests.get('https://api.nasa.gov/planetary/apod',params=data)
# create a dictionary for yesterday's picture
dict_day = result.json()
listofImageNames.append(dict_day['url'])
for imageName in listofImageNames:
display(Image(imageName))
gimmePictures(10)

Trying to take pictures with Coral camera with Coral edgeTPU dev board but it is really slow

To start with, I am not a developer, but a mere automation engineer that have worked a bit with coding in Java, python, C#, C++ and C.
I am trying to make a prototype that take pictures and stores them using a digital pin on the board. Atm I can take pictures using a switch, but it is really slow(around 3 seconds pr image).
My complete system is going to be like this:
A product passes by on a conveyor and a photo cell triggers the board to take an image and store it. If an operator removes a product(because of bad quality) the image is stored in a different folder.
I started with the snapshot function shipped with Mendel and have tried to get rid off the overhead, but the Gstream and pipeline-stuff confuses me a lot.
If someone could help me with how to understand the supplied code, or how to write a minimalistic solution to take an image i would be grateful :)
I have tried to understand and use project-teachable and examples-camera from Google coral https://github.com/google-coral, but with no luck. I have had the best luck with the snapshot tool that uses snapshot.py that are referenced here https://coral.withgoogle.com/docs/camera/datasheet/#snapshot-tool
from periphery import GPIO
import time
import argparse
import contextlib
import fcntl
import os
import select
import sys
import termios
import threading
import gi
gi.require_version('Gst', '1.0')
gi.require_version('GstBase', '1.0')
from functools import partial
from gi.repository import GLib, GObject, Gst, GstBase
from PIL import Image
GObject.threads_init()
Gst.init(None)
WIDTH = 2592
HEIGHT = 1944
FILENAME_PREFIX = 'img'
FILENAME_SUFFIX = '.png'
AF_SYSFS_NODE = '/sys/module/ov5645_camera_mipi_v2/parameters/ov5645_af'
CAMERA_INIT_QUERY_SYSFS_NODE = '/sys/module/ov5645_camera_mipi_v2/parameters/ov5645_initialized'
HDMI_SYSFS_NODE = '/sys/class/drm/card0/card0-HDMI-A-1/status'
# No of initial frames to throw away before camera has stabilized
SCRAP_FRAMES = 1
SRC_WIDTH = 2592
SRC_HEIGHT = 1944
SRC_RATE = '15/1'
SRC_ELEMENT = 'v4l2src'
SINK_WIDTH = 2592
SINK_HEIGHT = 1944
SINK_ELEMENT = ('appsink name=appsink sync=false emit-signals=true '
'max-buffers=1 drop=true')
SCREEN_SINK = 'glimagesink sync=false'
FAKE_SINK = 'fakesink sync=false'
SRC_CAPS = 'video/x-raw,format=YUY2,width={width},height={height},framerate={rate}'
SINK_CAPS = 'video/x-raw,format=RGB,width={width},height={height}'
LEAKY_Q = 'queue max-size-buffers=1 leaky=downstream'
PIPELINE = '''
{src_element} ! {src_caps} ! {leaky_q} ! tee name=t
t. ! {leaky_q} ! {screen_sink}
t. ! {leaky_q} ! videoconvert ! {sink_caps} ! {sink_element}
'''
def on_bus_message(bus, message, loop):
t = message.type
if t == Gst.MessageType.EOS:
loop.quit()
elif t == Gst.MessageType.WARNING:
err, debug = message.parse_warning()
sys.stderr.write('Warning: %s: %s\n' % (err, debug))
elif t == Gst.MessageType.ERROR:
err, debug = message.parse_error()
sys.stderr.write('Error: %s: %s\n' % (err, debug))
loop.quit()
return True
def on_new_sample(sink, snapinfo):
if not snapinfo.save_frame():
# Throw away the frame
return Gst.FlowReturn.OK
sample = sink.emit('pull-sample')
buf = sample.get_buffer()
result, mapinfo = buf.map(Gst.MapFlags.READ)
if result:
imgfile = snapinfo.get_filename()
caps = sample.get_caps()
width = WIDTH
height = HEIGHT
img = Image.frombytes('RGB', (width, height), mapinfo.data, 'raw')
img.save(imgfile)
img.close()
buf.unmap(mapinfo)
return Gst.FlowReturn.OK
def run_pipeline(snapinfo):
src_caps = SRC_CAPS.format(width=SRC_WIDTH, height=SRC_HEIGHT, rate=SRC_RATE)
sink_caps = SINK_CAPS.format(width=SINK_WIDTH, height=SINK_HEIGHT)
screen_sink = FAKE_SINK
pipeline = PIPELINE.format(
leaky_q=LEAKY_Q,
src_element=SRC_ELEMENT,
src_caps=src_caps,
sink_caps=sink_caps,
sink_element=SINK_ELEMENT,
screen_sink=screen_sink)
pipeline = Gst.parse_launch(pipeline)
appsink = pipeline.get_by_name('appsink')
appsink.connect('new-sample', partial(on_new_sample, snapinfo=snapinfo))
loop = GObject.MainLoop()
# Set up a pipeline bus watch to catch errors.
bus = pipeline.get_bus()
bus.add_signal_watch()
bus.connect('message', on_bus_message, loop)
# Connect the loop to the snaphelper
snapinfo.connect_loop(loop)
# Run pipeline.
pipeline.set_state(Gst.State.PLAYING)
try:
loop.run()
except:
pass
# Clean up.
pipeline.set_state(Gst.State.NULL)
while GLib.MainContext.default().iteration(False):
pass
class SnapHelper:
def __init__(self, sysfs, prefix='img', oneshot=True, suffix='jpg'):
self.prefix = prefix
self.oneshot = oneshot
self.suffix = suffix
self.snap_it = oneshot
self.num = 0
self.scrapframes = SCRAP_FRAMES
self.sysfs = sysfs
def get_filename(self):
while True:
filename = self.prefix + str(self.num).zfill(4) + '.' + self.suffix
self.num = self.num + 1
if not os.path.exists(filename):
break
return filename
#def check_af(self):
#try:
# self.sysfs.seek(0)
# v = self.sysfs.read()
# if int(v) != 0x10:
# print('NO Focus')
#except:
# pass
# def refocus(self):
# try:#
# self.sysfs.write('1')
# self.sysfs.flush()
# except:
# pass
def save_frame(self):
# We always want to throw away the initial frames to let the
# camera stabilize. This seemed empirically to be the right number
# when running on desktop.
if self.scrapframes > 0:
self.scrapframes = self.scrapframes - 1
return False
if self.snap_it:
self.snap_it = False
retval = True
else:
retval = False
if self.oneshot:
self.loop.quit()
return retval
def connect_loop(self, loop):
self.loop = loop
def take_picture(snap):
start_time = int(round(time.time()))
run_pipeline(snap)
print(time.time()- start_time)
def main():
button = GPIO(138, "in")
last_state = False
with open(AF_SYSFS_NODE, 'w+') as sysfs:
snap = SnapHelper(sysfs, 'test', 'oneshot', 'jpg')
sysfs.write('2')
while 1:
button_state = button.read()
if(button_state==True and last_state == False):
snap = SnapHelper(sysfs, 'test', 'oneshot', 'jpg')
take_picture(snap)
last_state = button_state
if __name__== "__main__":
main()
sys.exit()
Output is what i expect, but it is slow.
I switched to a USB-webcam and used the pygame library instead.

PyGtk Serialization

I am currently working on a Note taking app in pyGtk and have set up a TextView where a user can type and add text tags for Bold Underline and Italics.
However, when it comes to saving the formatted text I cannot figure out how to do so.
I am trying to save in Gtk's native tagset format however after using
tag_format = TextBuffer.register_serialize_tagset()
content = TextBuffer.serialize(self, tag_format, start,end)
I cannot write this to a file with
open(filename, 'w').write(content)
because I get an error which states that it cannot write in bytes and needs a string instead.
I am currently working on a Note taking app in pyGtk and have set up a TextView where a user can type and add text tags for Bold Underline and Italics.
However, when it comes to saving the formatted text I cannot figure out how to do so.
I am trying to save in Gtk's native tagset format however after using
tag_format = TextBuffer.register_serialize_tagset()
content = TextBuffer.serialize(self, tag_format, start,end)
I cannot write this to a file with
open(filename, 'w').write(content)
because I get an error which states that it cannot write in bytes and needs a string instead.
import gi
gi.require_version('Gtk', '3.0')
from gi.repository import Gtk, Pango
I am currently working on a Note taking app in pyGtk and have set up a TextView where a user can type and add text tags for Bold Underline and Italics.
However, when it comes to saving the formatted text I cannot figure out how to do so.
I am trying to save in Gtk's native tagset format however after using
tag_format = TextBuffer.register_serialize_tagset()
content = TextBuffer.serialize(self, tag_format, start,end)
I cannot write this to a file with
open(filename, 'w').write(content)
because I get an error which states that it cannot write in bytes and needs a string instead.
File "example.py", line 87, in save_file
open(filename, 'w').write(content)
TypeError: write() argument must be str, not bytes
Here is sample code you can run and test by typing and then saving
import gi
gi.require_version('Gtk', '3.0')
from gi.repository import Gtk, Pango
class MainWindow(Gtk.ApplicationWindow):
def __init__(self):
Gtk.Window.__init__(self, title = "TwoNote")
self.grid = Gtk.Grid()
self.toolbar = Gtk.Toolbar()
self.grid.add(self.toolbar)
#buttons for toolbar
self.button_bold = Gtk.ToggleToolButton()
self.button_italic = Gtk.ToggleToolButton()
self.button_underline = Gtk.ToggleToolButton()
self.button_save = Gtk.ToolButton()
self.button_open = Gtk.ToolButton()
self.mytext = TextSet(self.button_bold, self.button_italic, self.button_underline)
self.button_bold.set_icon_name("format-text-bold-symbolic")
self.toolbar.insert(self.button_bold, 0)
self.button_italic.set_icon_name("format-text-italic-symbolic")
self.toolbar.insert(self.button_italic, 1)
self.button_underline.set_icon_name("format-text-underline-symbolic")
self.toolbar.insert(self.button_underline, 2)
self.toolbar.insert(self.button_save, 3)
self.toolbar.insert(self.button_open, 4)
self.button_open.set_icon_name("document-open-data")
self.button_save.set_icon_name("document-save")
self.button_save.connect("clicked", self.save_file)
self.button_open.connect("clicked", self.open_file)
self.button_bold.connect("toggled", self.mytext.on_button_clicked, "Bold", self.button_italic, self.button_underline)
self.button_italic.connect("toggled", self.mytext.on_button_clicked, "Italic", self.button_bold, self.button_underline)
self.button_underline.connect("toggled", self.mytext.on_button_clicked, "Underline", self.button_bold, self.button_italic)
self.grid.attach_next_to(self.mytext, self.toolbar, Gtk.PositionType.BOTTOM, 10,30)
self.add(self.grid)
filename = "Untitled"
def open_file(self, widget):
open_dialog = Gtk.FileChooserDialog("Open an existing file", self, Gtk.FileChooserAction.OPEN,(Gtk.STOCK_CANCEL,Gtk.ResponseType.CANCEL,Gtk.STOCK_OPEN, Gtk.ResponseType.OK))
open_response = open_dialog.run()
if open_response == Gtk.ResponseType.OK:
filename = open_dialog.get_filename()
text = open(filename).read()
self.mytext.get_buffer().set_text(text)
open_dialog.destroy()
elif open_response == Gtk.ResponseType.CANCEL:
print("Cancel clicked")
open_dialog.destroy()
def save_file(self, widget):
savechooser = Gtk.FileChooserDialog('Save File', self, Gtk.FileChooserAction.SAVE, (Gtk.STOCK_CANCEL, Gtk.ResponseType.CANCEL, Gtk.STOCK_SAVE, Gtk.ResponseType.OK))
allfilter = Gtk.FileFilter()
allfilter.set_name('All files')
allfilter.add_pattern('*')
savechooser.add_filter(allfilter)
txtFilter = Gtk.FileFilter()
txtFilter.set_name('Text file')
txtFilter.add_pattern('*.txt')
savechooser.add_filter(txtFilter)
response = savechooser.run()
if response == Gtk.ResponseType.OK:
filename = savechooser.get_filename()
print(filename, 'selected.')
buf = self.mytext.get_buffer()
start, end = buf.get_bounds()
tag_format = buf.register_serialize_tagset()
content = buf.serialize(buf, tag_format, start, end)
try:
open(filename, 'w').write(content)
except SomeError as e:
print('Could not save %s: %s' % (filename, err))
savechooser.destroy()
elif response == Gtk.ResponseType.CANCEL:
print('Closed, file not saved.')
savechooser.destroy()
class TextSet(Gtk.TextView):
def __init__(self, buttonBold, buttonItalic, buttonUnderline, interval = 1 ):
# Textview Setup
Gtk.TextView.__init__(self)
self.set_vexpand(True)
self.set_indent(10)
self.set_top_margin(90)
self.set_left_margin(20)
self.set_right_margin(20)
self.set_wrap_mode(Gtk.WrapMode.CHAR)
self.tb = TextBuffer()
self.set_buffer(self.tb)
# Thread setup
self.button_bold = buttonBold
self.button_italic = buttonItalic
self.button_underline = buttonUnderline
def on_button_clicked(self, widget, tagname, widget1, widget2):
state = widget.get_active()
name = widget.get_icon_name()
bounds = self.tb.get_selection_bounds()
self.tagname = tagname
if(state):
widget1.set_active(False)
widget2.set_active(False)
#highlighting
if(len(bounds) != 0):
start, end = bounds
myIter = self.tb.get_iter_at_mark(self.tb.get_insert())
myTags = myIter.get_tags()
if(myTags == [] and state == True):
self.tb.apply_tag_by_name(tagname, start, end)
elif(myTags != [] and state == True):
self.tb.remove_all_tags(start, end)
self.tb.apply_tag_by_name(tagname, start, end)
else:
for i in range(len(myTags)):
if(myTags[i].props.name == tagname):
self.tb.remove_tag_by_name(tagname,start,end)
myTags = []
self.tb.markup(widget, tagname)
def mouse_clicked(self, window, event):
self.button_bold.set_active(False)
self.button_italic.set_active(False)
self.button_underline.set_active(False)
class TextBuffer(Gtk.TextBuffer):
def __init__(self):
Gtk.TextBuffer.__init__(self)
self.connect_after('insert-text', self.text_inserted)
# A list to hold our active tags
self.taglist_on = []
# Our Bold tag.
self.tag_bold = self.create_tag("Bold", weight=Pango.Weight.BOLD)
self.tag_none = self.create_tag("None", weight=Pango.Weight.NORMAL)
self.tag_italic = self.create_tag("Italic", style=Pango.Style.ITALIC)
self.tag_underline = self.create_tag("Underline", underline=Pango.Underline.SINGLE)
def get_iter_position(self):
return self.get_iter_at_mark(self.get_insert())
def markup(self, widget, tagname):
self.tag_name = tagname
self.check = True
''' add "bold" to our active tags list '''
if(widget.get_active() == True):
if(self.tag_name == 'Bold'):
if 'Bold' in self.taglist_on:
del self.taglist_on[self.taglist_on.index('Bold')]
else:
self.taglist_on.append('Bold')
if(self.tag_name == 'Italic'):
if 'Italic' in self.taglist_on:
del self.taglist_on[self.taglist_on.index('Italic')]
else:
self.taglist_on.append('Italic')
if(self.tag_name == 'Underline'):
if 'Underline' in self.taglist_on:
del self.taglist_on[self.taglist_on.index('Underline')]
else:
self.taglist_on.append('Underline')
else:
self.check = False
def text_inserted(self, buffer, iter, text, length):
# A text was inserted in the buffer. If there are ny tags in self.tags_on, apply them
#if self.taglist_None or self.taglist_Italic or self.taglist_Underline or self.taglist_Bold:
if self.taglist_on:
# This sets the iter back N characters
iter.backward_chars(length)
# And this applies tag from iter to end of buffer
if(self.check == True):
if(self.tag_name == 'Italic'):
self.apply_tag_by_name('Italic', self.get_iter_position(), iter)
if(self.tag_name == 'Bold'):
self.apply_tag_by_name('Bold', self.get_iter_position(), iter)
if(self.tag_name == 'Underline'):
self.apply_tag_by_name('Underline', self.get_iter_position(), iter)
else:
self.remove_all_tags(self.get_iter_position(), iter)
win = MainWindow()
win.connect("delete-event", Gtk.main_quit)
win.show_all()
Gtk.main()
I figured it out rather than using
open(filename, 'w').write(content)
to save the content I imported GLib and used
GLib.file_set_contents(filename, content)

how to determine which JPEG picture is corrupt in Tensorflow decode_jpeg

when i decode JPEG format pictures, it give message "corrupt jpeg data premature end of data segment ". how can i determine which picture is corrupt.
This is my code:
import os
import tensorflow as tf
directory = 'D:\\tfrecord\\read'
directories = []
class_names = []
photo_filenames = []
for filename in os.listdir(directory):
path = os.path.join(directory, filename)
photo_filenames.append(path)
with tf.Session() as sess:
print("session")
init = tf.global_variables_initializer()
sess.run(init)
for filename in photo_filenames:
filecontents = tf.read_file(filename)
image = tf.image.decode_jpeg(filecontents, channels = 3)
try:
sess.run(image)
except Exception as e:
print(filename)
print (e)
insert
image = tf.Print(image,[filename])
after
image = tf.image.decode_jpeg(filecontents, channels = 3)
the filename will show right after 'corrupt jpeg data...'

How do I convert a directory of jpeg images to TFRecords file in tensorflow?

I have training data that is a directory of jpeg images and a corresponding text file containing the file name and the associated category label. I am trying to convert this training data into a tfrecords file as described in the tensorflow documentation. I have spent quite some time trying to get this to work but there are no examples in tensorflow that demonstrate how to use any of the readers to read in jpeg files and add them to a tfrecord using tfrecordwriter
I hope this helps:
filename_queue = tf.train.string_input_producer(['/Users/HANEL/Desktop/tf.png']) # list of files to read
reader = tf.WholeFileReader()
key, value = reader.read(filename_queue)
my_img = tf.image.decode_png(value) # use decode_png or decode_jpeg decoder based on your files.
init_op = tf.initialize_all_variables()
with tf.Session() as sess:
sess.run(init_op)
# Start populating the filename queue.
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(coord=coord)
for i in range(1): #length of your filename list
image = my_img.eval() #here is your image Tensor :)
print(image.shape)
Image.show(Image.fromarray(np.asarray(image)))
coord.request_stop()
coord.join(threads)
For getting all images as an array of tensors use the following code example.
Github repo of ImageFlow
Update:
In the previous answer I just told how to read an image in TF format, but not saving it in TFRecords. For that you should use:
def _int64_feature(value):
return tf.train.Feature(int64_list=tf.train.Int64List(value=[value]))
def _bytes_feature(value):
return tf.train.Feature(bytes_list=tf.train.BytesList(value=[value]))
# images and labels array as input
def convert_to(images, labels, name):
num_examples = labels.shape[0]
if images.shape[0] != num_examples:
raise ValueError("Images size %d does not match label size %d." %
(images.shape[0], num_examples))
rows = images.shape[1]
cols = images.shape[2]
depth = images.shape[3]
filename = os.path.join(FLAGS.directory, name + '.tfrecords')
print('Writing', filename)
writer = tf.python_io.TFRecordWriter(filename)
for index in range(num_examples):
image_raw = images[index].tostring()
example = tf.train.Example(features=tf.train.Features(feature={
'height': _int64_feature(rows),
'width': _int64_feature(cols),
'depth': _int64_feature(depth),
'label': _int64_feature(int(labels[index])),
'image_raw': _bytes_feature(image_raw)}))
writer.write(example.SerializeToString())
More info here
And you read the data like this:
# Remember to generate a file name queue of you 'train.TFRecord' file path
def read_and_decode(filename_queue):
reader = tf.TFRecordReader()
_, serialized_example = reader.read(filename_queue)
features = tf.parse_single_example(
serialized_example,
dense_keys=['image_raw', 'label'],
# Defaults are not specified since both keys are required.
dense_types=[tf.string, tf.int64])
# Convert from a scalar string tensor (whose single string has
image = tf.decode_raw(features['image_raw'], tf.uint8)
image = tf.reshape(image, [my_cifar.n_input])
image.set_shape([my_cifar.n_input])
# OPTIONAL: Could reshape into a 28x28 image and apply distortions
# here. Since we are not applying any distortions in this
# example, and the next step expects the image to be flattened
# into a vector, we don't bother.
# Convert from [0, 255] -> [-0.5, 0.5] floats.
image = tf.cast(image, tf.float32)
image = tf.cast(image, tf.float32) * (1. / 255) - 0.5
# Convert label from a scalar uint8 tensor to an int32 scalar.
label = tf.cast(features['label'], tf.int32)
return image, label
Tensorflow's inception model has a file build_image_data.py that can accomplish the same thing with the assumption that each subdirectory represents a label.
Note that images will be saved in TFRecord as uncompressed tensors, possibly increasing the size by a factor of about 5. That's wasting storage space, and likely to be rather slow because of the amount of data that needs to be read.
It's far better to just save the filename in the TFRecord, and read the file on demand. The new Dataset API works well, and the documentation has this example:
# Reads an image from a file, decodes it into a dense tensor, and resizes it
# to a fixed shape.
def _parse_function(filename, label):
image_string = tf.read_file(filename)
image_decoded = tf.image.decode_jpeg(image_string)
image_resized = tf.image.resize_images(image_decoded, [28, 28])
return image_resized, label
# A vector of filenames.
filenames = tf.constant(["/var/data/image1.jpg", "/var/data/image2.jpg", ...])
# `labels[i]` is the label for the image in `filenames[i].
labels = tf.constant([0, 37, ...])
dataset = tf.data.Dataset.from_tensor_slices((filenames, labels))
dataset = dataset.map(_parse_function)
I have same problem, too.
So here is how i get the tfrecords files of my own jpeg files
Edit: add sol 1 - a better & faster way
update: Jan/5/2020
(Recommended) Solution 1: TFRecordWriter
See this Tfrecords Guide post
Solution 2:
From tensorflow official github: How to Construct a New Dataset for Retraining, use official python script build_image_data.py directly and bazel is a better idea.
Here is the instruction:
To run build_image_data.py, you can run the following command line:
# location to where to save the TFRecord data.
OUTPUT_DIRECTORY=$HOME/my-custom-data/
# build the preprocessing script.
bazel build inception/build_image_data
# convert the data.
bazel-bin/inception/build_image_data \
--train_directory="${TRAIN_DIR}" \
--validation_directory="${VALIDATION_DIR}" \
--output_directory="${OUTPUT_DIRECTORY}" \
--labels_file="${LABELS_FILE}" \
--train_shards=128 \
--validation_shards=24 \
--num_threads=8
where the $OUTPUT_DIRECTORY is the location of the sharded
TFRecords. The $LABELS_FILE will be a text file that is read by
the script that provides a list of all of the labels.
then, it should do the trick.
ps. bazel, which is made by Google, turn code into makefile.
Solution 3:
First, i reference the instruction by #capitalistpug and check the shell script file
(shell script file providing by Google: download_and_preprocess_flowers.sh)
Second, i also find out a mini inception-v3 training tutorial by NVIDIA
(NVIDIA official SPEED UP TRAINING WITH GPU-ACCELERATED TENSORFLOW)
Be careful, the following steps need to be executed in the Bazel WORKSAPCE enviroment
so Bazel build file can run successfully
First step, I comment out the part of downloading the imagenet data set that i already downloaded
and the rest of the part that i don't need of download_and_preprocess_flowers.sh
Second step, change directory to tensorflow/models/inception
where it is the Bazel environment and it is build by Bazel before
$ cd tensorflow/models/inception
Optional : If it is not builded before, type in the following code in cmd
$ bazel build inception/download_and_preprocess_flowers
You need to figure out the content in the following image
And last step, type in the following code:
$ bazel-bin/inception/download_and_preprocess_flowers $Your/own/image/data/path
Then, it will start calling build_image_data.py and creating tfrecords file
Try this script:
(used with VOC segmentation dataset:http://host.robots.ox.ac.uk/pascal/VOC/voc2012/)
import numpy as np
import tensorflow as tf
import scipy.io # to read .mat files
from PIL import Image # to read image files
def get_image(path):
jpg = Image.open(path).convert('RGB')
return np.array(jpg)
def get_label_png(path):
png = Image.open(path) # image is saved as palettised png.
arr = np.array(png)
return arr[..., None]
def get_example(image, label):
feature = {
'height': tf.train.Feature(int64_list=tf.train.Int64List(value=[image.shape[0]])),
'width': tf.train.Feature(int64_list=tf.train.Int64List(value=[image.shape[1]])),
'image': tf.train.Feature(bytes_list=tf.train.BytesList(value=[image.tobytes()])),
'label': tf.train.Feature(bytes_list=tf.train.BytesList(value=[label.tobytes()]))
}
return tf.train.Example(features=tf.train.Features(feature=feature))
## Paths ======================================
images_folder = 'data/images/' #images folder
labels_folder = 'data/labels/' #label folder
train_file = 'data/train.txt'
val_file = 'data/val.txt'
TRAIN = 'data/train.tfrecords'
VAL = 'data/val.tfrecords'
## write train dataset
with tf.io.TFRecordWriter(TRAIN) as writer:
with open(train_file) as file:
filenames = [s.rstrip('\n') for s in file.readlines()]
for name in filenames:
image = utils.get_image(images_folder+name+'.jpg')
label = utils.get_label_png(labels_folder+name+'.png')
writer.write(utils.get_example(image, label).SerializeToString())
## write validation dataset
with tf.io.TFRecordWriter(VAL) as writer:
with open(val_file) as file:
filenames = [s.rstrip('\n') for s in file.readlines()]
for name in filenames:
image = utils.get_image(images_folder+name+'.jpg')
label = utils.get_label_png(labels_folder+name+'.png')
writer.write(utils.get_example(image, label).SerializeToString())
Mentioning the Code in the Link specified by Kamil, so that the code will be available even if the Link is broken.
"""Converts image data to TFRecords file format with Example protos.
If your data set involves bounding boxes, please look at build_imagenet_data.py.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from datetime import datetime
import os
import random
import sys
import threading
import numpy as np
import tensorflow as tf
tf.app.flags.DEFINE_string('train_directory', '/tmp/',
'Training data directory')
tf.app.flags.DEFINE_string('validation_directory', '/tmp/',
'Validation data directory')
tf.app.flags.DEFINE_string('output_directory', '/tmp/',
'Output data directory')
tf.app.flags.DEFINE_integer('train_shards', 2,
'Number of shards in training TFRecord files.')
tf.app.flags.DEFINE_integer('validation_shards', 2,
'Number of shards in validation TFRecord files.')
tf.app.flags.DEFINE_integer('num_threads', 2,
'Number of threads to preprocess the images.')
# The labels file contains a list of valid labels are held in this file.
# Assumes that the file contains entries as such:
# dog
# cat
# flower
# where each line corresponds to a label. We map each label contained in
# the file to an integer corresponding to the line number starting from 0.
tf.app.flags.DEFINE_string('labels_file', '', 'Labels file')
FLAGS = tf.app.flags.FLAGS
def _int64_feature(value):
"""Wrapper for inserting int64 features into Example proto."""
if not isinstance(value, list):
value = [value]
return tf.train.Feature(int64_list=tf.train.Int64List(value=value))
def _bytes_feature(value):
"""Wrapper for inserting bytes features into Example proto."""
return tf.train.Feature(bytes_list=tf.train.BytesList(value=[value]))
def _convert_to_example(filename, image_buffer, label, text, height, width):
"""Build an Example proto for an example.
Args:
filename: string, path to an image file, e.g., '/path/to/example.JPG'
image_buffer: string, JPEG encoding of RGB image
label: integer, identifier for the ground truth for the network
text: string, unique human-readable, e.g. 'dog'
height: integer, image height in pixels
width: integer, image width in pixels
Returns:
Example proto
"""
colorspace = 'RGB'
channels = 3
image_format = 'JPEG'
example = tf.train.Example(features=tf.train.Features(feature={
'image/height': _int64_feature(height),
'image/width': _int64_feature(width),
'image/colorspace': _bytes_feature(tf.compat.as_bytes(colorspace)),
'image/channels': _int64_feature(channels),
'image/class/label': _int64_feature(label),
'image/class/text': _bytes_feature(tf.compat.as_bytes(text)),
'image/format': _bytes_feature(tf.compat.as_bytes(image_format)),
'image/filename': _bytes_feature(tf.compat.as_bytes(os.path.basename(filename))),
'image/encoded': _bytes_feature(tf.compat.as_bytes(image_buffer))}))
return example
class ImageCoder(object):
"""Helper class that provides TensorFlow image coding utilities."""
def __init__(self):
# Create a single Session to run all image coding calls.
self._sess = tf.Session()
# Initializes function that converts PNG to JPEG data.
self._png_data = tf.placeholder(dtype=tf.string)
image = tf.image.decode_png(self._png_data, channels=3)
self._png_to_jpeg = tf.image.encode_jpeg(image, format='rgb', quality=100)
# Initializes function that decodes RGB JPEG data.
self._decode_jpeg_data = tf.placeholder(dtype=tf.string)
self._decode_jpeg = tf.image.decode_jpeg(self._decode_jpeg_data, channels=3)
def png_to_jpeg(self, image_data):
return self._sess.run(self._png_to_jpeg,
feed_dict={self._png_data: image_data})
def decode_jpeg(self, image_data):
image = self._sess.run(self._decode_jpeg,
feed_dict={self._decode_jpeg_data: image_data})
assert len(image.shape) == 3
assert image.shape[2] == 3
return image
def _is_png(filename):
"""Determine if a file contains a PNG format image.
Args:
filename: string, path of the image file.
Returns:
boolean indicating if the image is a PNG.
"""
return '.png' in filename
def _process_image(filename, coder):
"""Process a single image file.
Args:
filename: string, path to an image file e.g., '/path/to/example.JPG'.
coder: instance of ImageCoder to provide TensorFlow image coding utils.
Returns:
image_buffer: string, JPEG encoding of RGB image.
height: integer, image height in pixels.
width: integer, image width in pixels.
"""
# Read the image file.
with tf.gfile.FastGFile(filename, 'rb') as f:
image_data = f.read()
# Convert any PNG to JPEG's for consistency.
if _is_png(filename):
print('Converting PNG to JPEG for %s' % filename)
image_data = coder.png_to_jpeg(image_data)
# Decode the RGB JPEG.
image = coder.decode_jpeg(image_data)
# Check that image converted to RGB
assert len(image.shape) == 3
height = image.shape[0]
width = image.shape[1]
assert image.shape[2] == 3
return image_data, height, width
def _process_image_files_batch(coder, thread_index, ranges, name, filenames,
texts, labels, num_shards):
"""Processes and saves list of images as TFRecord in 1 thread.
Args:
coder: instance of ImageCoder to provide TensorFlow image coding utils.
thread_index: integer, unique batch to run index is within [0, len(ranges)).
ranges: list of pairs of integers specifying ranges of each batches to
analyze in parallel.
name: string, unique identifier specifying the data set
filenames: list of strings; each string is a path to an image file
texts: list of strings; each string is human readable, e.g. 'dog'
labels: list of integer; each integer identifies the ground truth
num_shards: integer number of shards for this data set.
"""
# Each thread produces N shards where N = int(num_shards / num_threads).
# For instance, if num_shards = 128, and the num_threads = 2, then the first
# thread would produce shards [0, 64).
num_threads = len(ranges)
assert not num_shards % num_threads
num_shards_per_batch = int(num_shards / num_threads)
shard_ranges = np.linspace(ranges[thread_index][0],
ranges[thread_index][1],
num_shards_per_batch + 1).astype(int)
num_files_in_thread = ranges[thread_index][1] - ranges[thread_index][0]
counter = 0
for s in range(num_shards_per_batch):
# Generate a sharded version of the file name, e.g. 'train-00002-of-00010'
shard = thread_index * num_shards_per_batch + s
output_filename = '%s-%.5d-of-%.5d' % (name, shard, num_shards)
output_file = os.path.join(FLAGS.output_directory, output_filename)
writer = tf.python_io.TFRecordWriter(output_file)
shard_counter = 0
files_in_shard = np.arange(shard_ranges[s], shard_ranges[s + 1], dtype=int)
for i in files_in_shard:
filename = filenames[i]
label = labels[i]
text = texts[i]
try:
image_buffer, height, width = _process_image(filename, coder)
except Exception as e:
print(e)
print('SKIPPED: Unexpected eror while decoding %s.' % filename)
continue
example = _convert_to_example(filename, image_buffer, label,
text, height, width)
writer.write(example.SerializeToString())
shard_counter += 1
counter += 1
if not counter % 1000:
print('%s [thread %d]: Processed %d of %d images in thread batch.' %
(datetime.now(), thread_index, counter, num_files_in_thread))
sys.stdout.flush()
writer.close()
print('%s [thread %d]: Wrote %d images to %s' %
(datetime.now(), thread_index, shard_counter, output_file))
sys.stdout.flush()
shard_counter = 0
print('%s [thread %d]: Wrote %d images to %d shards.' %
(datetime.now(), thread_index, counter, num_files_in_thread))
sys.stdout.flush()
def _process_image_files(name, filenames, texts, labels, num_shards):
"""Process and save list of images as TFRecord of Example protos.
Args:
name: string, unique identifier specifying the data set
filenames: list of strings; each string is a path to an image file
texts: list of strings; each string is human readable, e.g. 'dog'
labels: list of integer; each integer identifies the ground truth
num_shards: integer number of shards for this data set.
"""
assert len(filenames) == len(texts)
assert len(filenames) == len(labels)
# Break all images into batches with a [ranges[i][0], ranges[i][1]].
spacing = np.linspace(0, len(filenames), FLAGS.num_threads + 1).astype(np.int)
ranges = []
for i in range(len(spacing) - 1):
ranges.append([spacing[i], spacing[i + 1]])
# Launch a thread for each batch.
print('Launching %d threads for spacings: %s' % (FLAGS.num_threads, ranges))
sys.stdout.flush()
# Create a mechanism for monitoring when all threads are finished.
coord = tf.train.Coordinator()
# Create a generic TensorFlow-based utility for converting all image codings.
coder = ImageCoder()
threads = []
for thread_index in range(len(ranges)):
args = (coder, thread_index, ranges, name, filenames,
texts, labels, num_shards)
t = threading.Thread(target=_process_image_files_batch, args=args)
t.start()
threads.append(t)
# Wait for all the threads to terminate.
coord.join(threads)
print('%s: Finished writing all %d images in data set.' %
(datetime.now(), len(filenames)))
sys.stdout.flush()
def _find_image_files(data_dir, labels_file):
"""Build a list of all images files and labels in the data set.
Args:
data_dir: string, path to the root directory of images.
Assumes that the image data set resides in JPEG files located in
the following directory structure.
data_dir/dog/another-image.JPEG
data_dir/dog/my-image.jpg
where 'dog' is the label associated with these images.
labels_file: string, path to the labels file.
The list of valid labels are held in this file. Assumes that the file
contains entries as such:
dog
cat
flower
where each line corresponds to a label. We map each label contained in
the file to an integer starting with the integer 0 corresponding to the
label contained in the first line.
Returns:
filenames: list of strings; each string is a path to an image file.
texts: list of strings; each string is the class, e.g. 'dog'
labels: list of integer; each integer identifies the ground truth.
"""
print('Determining list of input files and labels from %s.' % data_dir)
unique_labels = [l.strip() for l in tf.gfile.FastGFile(
labels_file, 'r').readlines()]
labels = []
filenames = []
texts = []
# Leave label index 0 empty as a background class.
label_index = 1
# Construct the list of JPEG files and labels.
for text in unique_labels:
jpeg_file_path = '%s/%s/*' % (data_dir, text)
matching_files = tf.gfile.Glob(jpeg_file_path)
labels.extend([label_index] * len(matching_files))
texts.extend([text] * len(matching_files))
filenames.extend(matching_files)
if not label_index % 100:
print('Finished finding files in %d of %d classes.' % (
label_index, len(labels)))
label_index += 1
# Shuffle the ordering of all image files in order to guarantee
# random ordering of the images with respect to label in the
# saved TFRecord files. Make the randomization repeatable.
shuffled_index = list(range(len(filenames)))
random.seed(12345)
random.shuffle(shuffled_index)
filenames = [filenames[i] for i in shuffled_index]
texts = [texts[i] for i in shuffled_index]
labels = [labels[i] for i in shuffled_index]
print('Found %d JPEG files across %d labels inside %s.' %
(len(filenames), len(unique_labels), data_dir))
return filenames, texts, labels
def _process_dataset(name, directory, num_shards, labels_file):
"""Process a complete data set and save it as a TFRecord.
Args:
name: string, unique identifier specifying the data set.
directory: string, root path to the data set.
num_shards: integer number of shards for this data set.
labels_file: string, path to the labels file.
"""
filenames, texts, labels = _find_image_files(directory, labels_file)
_process_image_files(name, filenames, texts, labels, num_shards)
def main(unused_argv):
assert not FLAGS.train_shards % FLAGS.num_threads, (
'Please make the FLAGS.num_threads commensurate with FLAGS.train_shards')
assert not FLAGS.validation_shards % FLAGS.num_threads, (
'Please make the FLAGS.num_threads commensurate with '
'FLAGS.validation_shards')
print('Saving results to %s' % FLAGS.output_directory)
# Run it!
_process_dataset('validation', FLAGS.validation_directory,
FLAGS.validation_shards, FLAGS.labels_file)
_process_dataset('train', FLAGS.train_directory,
FLAGS.train_shards, FLAGS.labels_file)
if __name__ == '__main__':
tf.app.run()
In case of too much size in tfrecord files you use directly read bytes.
This link shows it.
TFrecords occupy more space than original JPEG images
you use this function to read bytes directly.
img_bytes = open(path,'rb').read()
reference
https://github.com/tensorflow/tensorflow/issues/9675
You can use the Kubeflow pipeline here to do the conversion:
https://aihub.cloud.google.com/u/0/p/products%2Fded3e5e5-d2e8-4d65-9b9f-5ffaa9a27ea1
Click on the Download link (create a Kubeflow cluster to run the pipeline)