Merge pull request #30 from elephant-track/dev

ELEPHANT server v0.5.4 -> v0.5.5

Dockerfile-test

@@ -1,4 +1,4 @@
-FROM elephant-server:0.5.4
+FROM elephant-server:0.5.6
 
 LABEL maintainer="Ko Sugawara <[email protected]>"
 

Makefile

@@ -5,7 +5,7 @@ help:
 
 ELEPHANT_GPU?=all
 ELEPHANT_WORKSPACE?=${PWD}/workspace
-ELEPHANT_IMAGE_NAME?=elephant-server:0.5.4
+ELEPHANT_IMAGE_NAME?=elephant-server:0.5.6
 ELEPHANT_NVIDIA_GID?=$$(ls -n /dev/nvidia0 2>/dev/null | awk '{print $$4}')
 ELEPHANT_DOCKER?=docker
 ELEPHANT_RABBITMQ_NODENAME?=rabbit@localhost

docker/install-rabbitmq.sh

@@ -8,23 +8,31 @@ apt-get install curl gnupg debian-keyring debian-archive-keyring apt-transport-h
 ## Ignore warnings
 export APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=1
 ## Team RabbitMQ's main signing key
-apt-key adv --keyserver "hkps://keys.openpgp.org" --recv-keys "0x0A9AF2115F4687BD29803A206B73A36E6026DFCA"
-## Cloudsmith: modern Erlang repository
-curl -1sLf https://dl.cloudsmith.io/public/rabbitmq/rabbitmq-erlang/gpg.E495BB49CC4BBE5B.key | apt-key add -
-## Cloudsmith: RabbitMQ repository
-curl -1sLf https://dl.cloudsmith.io/public/rabbitmq/rabbitmq-server/gpg.9F4587F226208342.key | apt-key add -
+curl -1sLf "https://keys.openpgp.org/vks/v1/by-fingerprint/0A9AF2115F4687BD29803A206B73A36E6026DFCA" | sudo gpg --dearmor | sudo tee /usr/share/keyrings/com.rabbitmq.team.gpg > /dev/null
+## Community mirror of Cloudsmith: modern Erlang repository
+curl -1sLf https://github.com/rabbitmq/signing-keys/releases/download/3.0/cloudsmith.rabbitmq-erlang.E495BB49CC4BBE5B.key | sudo gpg --dearmor | sudo tee /usr/share/keyrings/rabbitmq.E495BB49CC4BBE5B.gpg > /dev/null
+## Community mirror of Cloudsmith: RabbitMQ repository
+curl -1sLf https://github.com/rabbitmq/signing-keys/releases/download/3.0/cloudsmith.rabbitmq-server.9F4587F226208342.key | sudo gpg --dearmor | sudo tee /usr/share/keyrings/rabbitmq.9F4587F226208342.gpg > /dev/null
 
 ## Add apt repositories maintained by Team RabbitMQ
-tee /etc/apt/sources.list.d/rabbitmq.list <<EOF
+sudo tee /etc/apt/sources.list.d/rabbitmq.list <<EOF
 ## Provides modern Erlang/OTP releases
 ##
-deb https://dl.cloudsmith.io/public/rabbitmq/rabbitmq-erlang/deb/ubuntu bionic main
-deb-src https://dl.cloudsmith.io/public/rabbitmq/rabbitmq-erlang/deb/ubuntu bionic main
+deb [signed-by=/usr/share/keyrings/rabbitmq.E495BB49CC4BBE5B.gpg] https://ppa1.novemberain.com/rabbitmq/rabbitmq-erlang/deb/ubuntu jammy main
+deb-src [signed-by=/usr/share/keyrings/rabbitmq.E495BB49CC4BBE5B.gpg] https://ppa1.novemberain.com/rabbitmq/rabbitmq-erlang/deb/ubuntu jammy main
+
+# another mirror for redundancy
+deb [signed-by=/usr/share/keyrings/rabbitmq.E495BB49CC4BBE5B.gpg] https://ppa2.novemberain.com/rabbitmq/rabbitmq-erlang/deb/ubuntu jammy main
+deb-src [signed-by=/usr/share/keyrings/rabbitmq.E495BB49CC4BBE5B.gpg] https://ppa2.novemberain.com/rabbitmq/rabbitmq-erlang/deb/ubuntu jammy main
 
 ## Provides RabbitMQ
 ##
-deb https://dl.cloudsmith.io/public/rabbitmq/rabbitmq-server/deb/ubuntu bionic main
-deb-src https://dl.cloudsmith.io/public/rabbitmq/rabbitmq-server/deb/ubuntu bionic main
+deb [signed-by=/usr/share/keyrings/rabbitmq.9F4587F226208342.gpg] https://ppa1.novemberain.com/rabbitmq/rabbitmq-server/deb/ubuntu jammy main
+deb-src [signed-by=/usr/share/keyrings/rabbitmq.9F4587F226208342.gpg] https://ppa1.novemberain.com/rabbitmq/rabbitmq-server/deb/ubuntu jammy main
+
+# another mirror for redundancy
+deb [signed-by=/usr/share/keyrings/rabbitmq.9F4587F226208342.gpg] https://ppa2.novemberain.com/rabbitmq/rabbitmq-server/deb/ubuntu jammy main
+deb-src [signed-by=/usr/share/keyrings/rabbitmq.9F4587F226208342.gpg] https://ppa2.novemberain.com/rabbitmq/rabbitmq-server/deb/ubuntu jammy main
 EOF
 
 ## Update package indices

elephant-core/elephant/datasets.py

@@ -57,8 +57,7 @@ def profile(func):
         return func
 
 
-def _load_image(za_input, timepoint, use_median=False, img_size=None):
-    img = za_input[timepoint].astype('float32')
+def _load_image(img, use_median=False, img_size=None):
     if use_median and img.ndim == 3:
         global_median = np.median(img)
         for z in range(img.shape[0]):
@@ -86,38 +85,37 @@ def _get_memmap_or_load(za, timepoint, memmap_dir=None, use_median=False,
         fpath = Path(memmap_dir) / f'{key}.dat'
         lock = FileLock(str(fpath) + '.lock')
         with lock:
-            if not fpath.exists():
-                logger().info(f'creating {fpath}')
-                fpath.parent.mkdir(parents=True, exist_ok=True)
+            if not fpath_org.exists():
+                logger().info(f'creating {fpath_org}')
+                fpath_org.parent.mkdir(parents=True, exist_ok=True)
                 img_org = np.memmap(
                     fpath_org,
                     dtype='float32',
                     mode='w+',
                     shape=za.shape[1:]
                 )
                 img_org[:] = za[timepoint].astype('float32')
-                if img_size is None:
-                    img = img_org
-                else:
-                    img = np.memmap(
-                        fpath,
-                        dtype='float32',
-                        mode='w+',
-                        shape=img_size
-                    )
-                    img[:] = F.interpolate(
-                        torch.from_numpy(img_org)[None, None],
-                        size=img_size,
-                        mode='trilinear' if img.ndim == 3 else 'bilinear',
-                        align_corners=True,
-                    )[0, 0].numpy()
-                if use_median and img.ndim == 3:
-                    global_median = np.median(img)
-                    for z in range(img.shape[0]):
-                        slice_median = np.median(img[z])
-                        if 0 < slice_median:
-                            img[z] -= slice_median - global_median
-                img = normalize_zero_one(img)
+            else:
+                img_org = np.memmap(
+                    fpath_org,
+                    dtype='float32',
+                    mode='c',
+                    shape=za.shape[1:]
+                )
+            if not fpath.exists():
+                logger().info(f'creating {fpath}')
+                fpath.parent.mkdir(parents=True, exist_ok=True)
+                img = np.memmap(
+                    fpath,
+                    dtype='float32',
+                    mode='w+',
+                    shape=img_size
+                )
+                img[:] = _load_image(
+                    img_org,
+                    use_median=use_median,
+                    img_size=img_size,
+                )
             logger().info(f'loading from {fpath}')
             return np.memmap(
                 fpath,
@@ -126,14 +124,11 @@ def _get_memmap_or_load(za, timepoint, memmap_dir=None, use_median=False,
                 shape=za.shape[1:] if img_size is None else img_size
             )
     else:
-        img = za[timepoint].astype('float32')
-        if use_median and img.ndim == 3:
-            global_median = np.median(img)
-            for z in range(img.shape[0]):
-                slice_median = np.median(img[z])
-                if 0 < slice_median:
-                    img[z] -= slice_median - global_median
-        img = normalize_zero_one(img)
+        img = _load_image(
+            za[timepoint].astype('float32'),
+            use_median=use_median,
+            img_size=img_size,
+        )
     return img
 
 

elephant-core/elephant/version.py

@@ -24,4 +24,4 @@
 # ==============================================================================
 """Version definition."""
 
-__version__ = "0.5.4"
+__version__ = "0.5.6"

elephant_server.ipynb

@@ -39,7 +39,7 @@
       },
       "outputs": [],
       "source": [
-        "%env ELEPHANT_SERVER_VERSION = v0.5.4"
+        "%env ELEPHANT_SERVER_VERSION = v0.5.6"
       ]
     },
     {