From 0150865f9ca01349152a8c7b6c6ddb912c602f33 Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Mon, 29 Apr 2024 19:10:18 +0200 Subject: [PATCH 01/13] Update dcp_server_installation.rst --- docs/source/dcp_server_installation.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/source/dcp_server_installation.rst b/docs/source/dcp_server_installation.rst index 823f97a..897a2df 100644 --- a/docs/source/dcp_server_installation.rst +++ b/docs/source/dcp_server_installation.rst @@ -15,10 +15,11 @@ The client and server communicate via the `bentoml 3.8 and <3.12 (pyradiomics currently doesn't work with 3.12). Before starting make sure you have navigated to ``data-centric-platform/src/server``. All future steps expect you are in the server directory. In your dedicated environment run: .. code-block:: bash + pip install numpy # if you don't perform this step pyradiomics fails pip install -e ".[dev]" Launch DCP Server From 3c5f4d7a846f722506266093af6c0c54916b746c Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Mon, 29 Apr 2024 19:11:55 +0200 Subject: [PATCH 02/13] Update README.md --- src/server/README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/src/server/README.md b/src/server/README.md index 4c19dad..c2935ae 100644 --- a/src/server/README.md +++ b/src/server/README.md @@ -18,6 +18,7 @@ pip install dcp_server ### Installation for developers Before starting make sure you have navigated to ```data-centric-platform/src/server```. All future steps expect you are in the server directory. In your dedicated environment run: ``` +pip install numpy # if you don't do this, pyradiomics fails pip install -e . ``` From a924daae9260f91a0299128a67bfb5a1ac4542cf Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Tue, 30 Apr 2024 11:51:22 +0200 Subject: [PATCH 03/13] Update README.md --- src/server/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/server/README.md b/src/server/README.md index c2935ae..62a5e8b 100644 --- a/src/server/README.md +++ b/src/server/README.md @@ -16,7 +16,7 @@ pip install dcp_server ``` ### Installation for developers -Before starting make sure you have navigated to ```data-centric-platform/src/server```. All future steps expect you are in the server directory. In your dedicated environment run: +Before starting make sure you have navigated to ```data-centric-platform/src/server```. All future steps expect you are in the server directory. You will need to have Python <3.12. In your dedicated environment run: ``` pip install numpy # if you don't do this, pyradiomics fails pip install -e . From 0dd3ac1621300d0511928ce3e9fbe5a22733e5f5 Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Tue, 30 Apr 2024 11:57:56 +0200 Subject: [PATCH 04/13] Update README.md --- src/client/README.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/client/README.md b/src/client/README.md index ce0e435..027dd6f 100644 --- a/src/client/README.md +++ b/src/client/README.md @@ -21,8 +21,13 @@ pip install -e . #### Launch DCP client Make sure the server is already running, either locally or remotely. Then, depending on the configuration, simply run: ``` -dcp-client --mode local/remote +dcp-client --mode local ``` +or +``` +dcp-client --mode remote +``` +depending on whether your server is running locally or remotely. ## Want to know more? Visit our [documentation](https://data-centric-platform.readthedocs.io/en/latest/dcp_client_installation.html) for more information and a step by step guide on how to run the client. From 059ba386af7b0e1b1513d13e940ec5caf1ea768c Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Tue, 30 Apr 2024 11:59:44 +0200 Subject: [PATCH 05/13] Update dcp_client_installation.rst --- docs/source/dcp_client_installation.rst | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/docs/source/dcp_client_installation.rst b/docs/source/dcp_client_installation.rst index b4a883b..247415c 100644 --- a/docs/source/dcp_client_installation.rst +++ b/docs/source/dcp_client_installation.rst @@ -31,7 +31,14 @@ After you are certain the server is running, simply run: .. code-block:: bash - dcp-client --mode local/remote + dcp-client --mode local + + or + + .. code-block:: bash + + dcp-client --mode remote + Set the ``--mode`` argument to ``local`` or ``remote`` depending on which setup you have chosen for the server. From 43ac8c77ac42afea7acd52a74efe40a272e426c5 Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Tue, 30 Apr 2024 12:00:30 +0200 Subject: [PATCH 06/13] Update dcp_client_installation.rst --- docs/source/dcp_client_installation.rst | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/docs/source/dcp_client_installation.rst b/docs/source/dcp_client_installation.rst index 247415c..7355be4 100644 --- a/docs/source/dcp_client_installation.rst +++ b/docs/source/dcp_client_installation.rst @@ -67,12 +67,9 @@ Set the ``--mode`` argument to ``local`` or ``remote`` depending on which setup This folder is intended to contain images along with their final segmentations. **Only** move images here when the segmentation is complete and finalised, you won't be able to change them after they have been moved here. These are then used for training your model. -3. **Setting paths** -~~~~~~~~~~~~~~~~~~~~~ - After setting the paths for these three folders, you can click the **Start** button. If you have set the server configuration to the cloud, you will receive a message notifying you that your data will be uploaded to the cloud. Click **Ok** to continue. -4. **Data Overview** +3. **Data Overview** ~~~~~~~~~~~~~~~~~~~~ The main working window will appear next. This gives you an overview of the directories selected in the previous step along with three options: @@ -86,7 +83,7 @@ Set the ``--mode`` argument to ``local`` or ``remote`` depending on which setup :height: 200 :align: center -5. **The viewer** +4. **The viewer** ~~~~~~~~~~~~~~~~~~~~ In DCP, we use [napari](https://napari.org/stable) for viewing our images and masks, adding, editing or removing labels. An example of the viewer can be seen below. After adding or removing any objects and editing existing objects wherever necessary, there are two options available: From dc8c5757ccfc03f46d68d8620a37c48531f2f116 Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Tue, 30 Apr 2024 12:16:15 +0200 Subject: [PATCH 07/13] Update dcp_client_installation.rst --- docs/source/dcp_client_installation.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/dcp_client_installation.rst b/docs/source/dcp_client_installation.rst index 7355be4..f501733 100644 --- a/docs/source/dcp_client_installation.rst +++ b/docs/source/dcp_client_installation.rst @@ -25,7 +25,7 @@ Running the client: A step-by-step guide! DCP includes a client and server side for using our data centric platform. The client and server communicate via the `bentoml `_ library. There are currently two options available: running the server locally, or connecting to the running instance on the FZJ jusuf-cloud. - Before continuing, you need to make sure that DCP server is running, either locally or on the cloud. See :doc: `dcp_server_installation` for instructions on how to launch the server. **Note:** In order for this connection to succeed, you will need to have contacted the team developing DCP, so they can add your IP to the list of accepted requests. + Before continuing, you need to make sure that DCP server is running, either locally or on the cloud. See :ref:`DCP Client` for instructions on how to launch the server. **Note:** In order for this connection to succeed, you will need to have contacted the team developing DCP, so they can add your IP to the list of accepted requests. After you are certain the server is running, simply run: @@ -86,7 +86,7 @@ Set the ``--mode`` argument to ``local`` or ``remote`` depending on which setup 4. **The viewer** ~~~~~~~~~~~~~~~~~~~~ - In DCP, we use [napari](https://napari.org/stable) for viewing our images and masks, adding, editing or removing labels. An example of the viewer can be seen below. After adding or removing any objects and editing existing objects wherever necessary, there are two options available: + In DCP, we use `napari `_ for viewing our images and masks, adding, editing or removing labels. An example of the viewer can be seen below. After adding or removing any objects and editing existing objects wherever necessary, there are two options available: - Click the **Move to Curation in progress folder** if you are not 100% certain about the labels you have created. You can also click on the label in the labels layer and change the name. This will result in several label files being created in the *In progress folder*, which can be examined later on. **Note:** When changing the layer name in Napari, the user should rename it such that they add their initials or any other new info after _seg. E.g., if the labels of 1_seg.tiff have been changed in the Napari viewer, then the appropriate naming would for example be: 1_seg_CB.tiff and not 1_CB_seg.tiff. - Click the **Move to Curated dataset folder** if you are certain that the labels you are now viewing are final and require no more curation. These images and labels will later be used for training the machine learning model, so make sure that you select this option only if you are certain about the labels. If several labels are displayed (opened from the 'Curation in progress' step), make sure to **click** on the single label in the labels layer list you wish to be moved to the *Curated data folder*. The other images will then be automatically deleted from this folder. From a8b2f7abd81680023a058930b14de9d6bceacec8 Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Tue, 30 Apr 2024 12:21:32 +0200 Subject: [PATCH 08/13] Update README.md --- src/server/README.md | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/src/server/README.md b/src/server/README.md index 62a5e8b..46bea9c 100644 --- a/src/server/README.md +++ b/src/server/README.md @@ -9,20 +9,27 @@ The client and server communicate via the [bentoml](https://www.bentoml.com/?gcl ## How to use? -### Installation -This has been tested on Python versions 3.9, 3.10 and 3.11 on latest versions of Windows, Ubuntu and MacOS. In your dedicated environment run: +### Installation for developers + +For installing dcp-server you will need to have Python <3.12, the repo has been tested on Python versions 3.9, 3.10 and 3.11 on latest versions of Windows, Ubuntu and MacOS. + +First clone the repo: ``` -pip install dcp_server +git clone https://github.com/HelmholtzAI-Consultants-Munich/data-centric-platform.git ``` -### Installation for developers -Before starting make sure you have navigated to ```data-centric-platform/src/server```. All future steps expect you are in the server directory. You will need to have Python <3.12. In your dedicated environment run: +Then navigate to the server directory: +``` +cd data-centric-platform/src/server +``` + +In your dedicated environment run: ``` pip install numpy # if you don't do this, pyradiomics fails pip install -e . ``` -#### Launch DCP server +### Launch DCP server Simply run: ``` python dcp_server/main.py From 3233f73c361b09ecd26c84598e77a645e3d0e50c Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Tue, 30 Apr 2024 12:24:07 +0200 Subject: [PATCH 09/13] Update dcp_server_installation.rst --- docs/source/dcp_server_installation.rst | 22 +++++++++++++++++++--- 1 file changed, 19 insertions(+), 3 deletions(-) diff --git a/docs/source/dcp_server_installation.rst b/docs/source/dcp_server_installation.rst index 897a2df..15f81f5 100644 --- a/docs/source/dcp_server_installation.rst +++ b/docs/source/dcp_server_installation.rst @@ -15,12 +15,28 @@ The client and server communicate via the `bentoml 3.8 and <3.12 (pyradiomics currently doesn't work with 3.12). Before starting make sure you have navigated to ``data-centric-platform/src/server``. All future steps expect you are in the server directory. In your dedicated environment run: +For installing dcp-server you will need to have Python <3.12, the repo has been tested on Python versions 3.9, 3.10 and 3.11 on latest versions of Windows, Ubuntu and MacOS. + +First clone the repo: + +.. code-block:: bash + + git clone https://github.com/HelmholtzAI-Consultants-Munich/data-centric-platform.git + +Then navigate to the server directory: .. code-block:: bash - pip install numpy # if you don't perform this step pyradiomics fails - pip install -e ".[dev]" + cd data-centric-platform/src/server + + +In your dedicated environment run: + +.. code-block:: bash + + pip install numpy + pip install -e . + Launch DCP Server ------------------ From 28865fd4d2173ba81a8a1d7fe6ee01dc7832bd82 Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Tue, 30 Apr 2024 12:24:26 +0200 Subject: [PATCH 10/13] Update README.md --- src/server/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/server/README.md b/src/server/README.md index 46bea9c..24af07e 100644 --- a/src/server/README.md +++ b/src/server/README.md @@ -25,7 +25,7 @@ cd data-centric-platform/src/server In your dedicated environment run: ``` -pip install numpy # if you don't do this, pyradiomics fails +pip install numpy pip install -e . ``` From 871a493ec38064b050d57ca731c336959e1bd696 Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Tue, 30 Apr 2024 12:26:30 +0200 Subject: [PATCH 11/13] Update README.md --- src/client/README.md | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/src/client/README.md b/src/client/README.md index 027dd6f..71c48f2 100644 --- a/src/client/README.md +++ b/src/client/README.md @@ -6,18 +6,28 @@ The client of our data centric platform for microscopy imaging. ## How to use? -### Installation -This has been tested on Python versions 3.9, 3.10 and 3.11 on latest versions of Windows, Ubuntu and MacOS. In your dedicated environment run: +### Installation + +For installing dcp-client you will first need to clone the repo: + +``` +git clone https://github.com/HelmholtzAI-Consultants-Munich/data-centric-platform.git +``` + +Then navigate to the client directory: ``` -pip install dcp_client +cd data-centric-platform/src/client ``` -### Installation for developers -Before starting, make sure you have navigated to ```data-centric-platform/src/client```. All future steps expect you are in the client directory. This installation has been tested using a conda environment with python version 3.9 on a mac local machine. In your dedicated environment run: +In your dedicated environment run: ``` pip install -e . ``` +This installation has been thoroughly tested using a conda environment with python version 3.9, 3.10, 3.11 on a macOS local machine. + + + #### Launch DCP client Make sure the server is already running, either locally or remotely. Then, depending on the configuration, simply run: ``` From 3d4ee3d3a194b4ad629b726c8e75604806c3b7bf Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Tue, 30 Apr 2024 12:27:44 +0200 Subject: [PATCH 12/13] Update dcp_client_installation.rst --- docs/source/dcp_client_installation.rst | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/docs/source/dcp_client_installation.rst b/docs/source/dcp_client_installation.rst index f501733..7df4520 100644 --- a/docs/source/dcp_client_installation.rst +++ b/docs/source/dcp_client_installation.rst @@ -11,12 +11,28 @@ The client of our data centric platform for microscopy imaging. Installation ------------- -Before starting make sure you have navigated to ``data-centric-platform/src/client``. All future steps expect you are in the client directory. This installation has been tested using a conda environment with python version 3.9 on a mac local machine. In your dedicated environment run: +For installing dcp-client you will first need to clone the repo: + +.. code-block:: bash + + git clone https://github.com/HelmholtzAI-Consultants-Munich/data-centric-platform.git + + +Then navigate to the client directory: + +.. code-block:: bash + + cd data-centric-platform/src/client + +In your dedicated environment run: .. code-block:: bash pip install -e . + +This installation has been thoroughly tested using a conda environment with python version 3.9, 3.10, 3.11 and 3.12 on a macOS local machine. + Running the client: A step-by-step guide! ------------------------------------------ From 194408c912899c4cc9be075447f7b2c5568c93e0 Mon Sep 17 00:00:00 2001 From: Christina Bukas <31160776+christinab12@users.noreply.github.com> Date: Tue, 30 Apr 2024 12:28:23 +0200 Subject: [PATCH 13/13] Update README.md --- src/client/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/client/README.md b/src/client/README.md index 71c48f2..83fa27b 100644 --- a/src/client/README.md +++ b/src/client/README.md @@ -24,7 +24,7 @@ In your dedicated environment run: pip install -e . ``` -This installation has been thoroughly tested using a conda environment with python version 3.9, 3.10, 3.11 on a macOS local machine. +This installation has been thoroughly tested using a conda environment with python version 3.9, 3.10, 3.11 and 3.12 on a macOS local machine.