[NVIDIA] Removing hardcoded contributions and adding NVIDIA installation instructions

admin/run.sh

@@ -0,0 +1 @@
+./startup/fl_admin.sh

admin/startup/client.crt

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+-----BEGIN CERTIFICATE-----
+MIICwDCCAaigAwIBAgIUauNRWLVOu7xqbEe5qRXMfkgplb4wDQYJKoZIhvcNAQEL
+BQAwGjEYMBYGA1UEAwwPZXhhbXBsZV9wcm9qZWN0MB4XDTIwMTExODE5NDEzM1oX
+DTIxMTExMzE5NDEzM1owGjEYMBYGA1UEAwwPZW1haWxAaGVsbG8uY29tMIIBIjAN
+BgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAsCbJMZtbdSJCYUcpT8fJ372hf6ZH
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+q21ca5rTOeEE2+xu5Rgq78eCqKGgX5/kFXGO6KpVIa+7Ut/B
+-----END CERTIFICATE-----

admin/startup/client.key

@@ -0,0 +1,27 @@
+-----BEGIN RSA PRIVATE KEY-----
+MIIEpAIBAAKCAQEAsCbJMZtbdSJCYUcpT8fJ372hf6ZHciP608eOmu24GoaxW8fc
+Lsd4bQCcoSUtt4EmQJCZrM/Jf9wsRMl/p7Mg9eGJHgA6Hp44eGTiLjs6iCgkiC86
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+Qe405bfyFPLL0XI9ylvL5I77QqdBmsKTsynJpjoFjYlIJSMTvaTn6HzUvzL/JtrU
+RE0Zqn8QaR7VNIEnAs5+YoGpqeiLePFQyGCHpcDCr35HDbwThubcoA==
+-----END RSA PRIVATE KEY-----

admin/startup/docker.sh

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
+# docker run script for FL admin
+# to use host network, use line below
+NETARG="--net=host"
+# Admin clients do not need to open ports, so the following line is not needed.
+#NETARG="-p 8003:8003"
+DOCKER_IMAGE=clara-test
+# DOCKER_IMAGE=clara-test
+echo "Starting docker with $DOCKER_IMAGE"
+docker run --rm -it --name=fladmin -v $DIR/..:/workspace/ -w /workspace/ --shm-size=1g --ulimit memlock=-1 --ulimit stack=67108864 $NETARG $DOCKER_IMAGE /bin/bash

admin/startup/fl_admin.sh

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+#!/usr/bin/env bash
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+mkdir -p $DIR/../transfer
+python -m dlmed.hci.tools.admin --host localhost --port 8003 --prompt "> " --with_file_transfer --upload_dir=$DIR/../transfer --download_dir=$DIR/../transfer --with_shell --with_login --with_ssl --cred_type cert --ca_cert=$DIR/rootCA.pem --client_cert=$DIR/client.crt --client_key=$DIR/client.key

admin/startup/readme.txt

@@ -0,0 +1,20 @@
+*********************************
+Admin Client package
+*********************************
+The package includes the following files:
+readme.txt
+rootCA.pem
+client.crt
+client.key
+fl_admin.sh
+fl_admin.bat
+clara_hci-3.1.0-py3-none-any.whl
+
+Please install the clara_hci-3.1.0-py3-none-any.whl file by 'python3 -m pip install.'  This will install a set of Python codes
+in your environment.  After installation, you can run the fl_admin.sh or fl_admin.bat file to start communicating to the admin server.
+
+The rootCA.pem file is pointed by "ca_cert" in fl_admin.sh/fl_admin.bat.  If you plan to move/copy it to a different place,
+you will need to modify fl_admin.sh.  The same applies to the other two files, client.crt and client.key.
+
+The email in your submission to participate this Federated Learning project is embedded in the CN field of client
+ certificate, which uniquely identifies the participant.  As such, please safeguard its private key, client.key.

admin/startup/rootCA.pem

@@ -0,0 +1,19 @@
+-----BEGIN CERTIFICATE-----
+MIIDEjCCAfqgAwIBAgIUTdQtq75ym/mUZIqnDiCq0yhZQegwDQYJKoZIhvcNAQEL
+BQAwGjEYMBYGA1UEAwwPZXhhbXBsZV9wcm9qZWN0MB4XDTIwMTExODE5NDEzM1oX
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+99CjGZbx0lgyPVxLMWg0aSx1/fwDNQ==
+-----END CERTIFICATE-----

admin/transfer/custom_ct_spleen/config/config_cross_site_validation.json

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+{
+    "batch_size": 1,
+    "DATA_LIST_KEY": "validation",
+
+    "pre_transforms":
+    [
+        {
+            "name": "LoadNifti",
+            "args": {
+              "fields": "image"
+            }
+        },
+        {
+            "name": "ConvertToChannelsFirst",
+            "args": {
+              "fields": "image"
+            }
+        },
+        {
+            "name": "ScaleIntensityRange",
+            "args": {
+              "fields": "image",
+              "a_min": -57,
+              "a_max": 164,
+              "b_min": 0.0,
+              "b_max": 1.0,
+              "clip": true
+            }
+        }
+    ],
+
+    "post_transforms":
+    [
+        {
+            "name": "ArgmaxAcrossChannels",
+            "args": {
+              "fields": "model"
+            }
+        },
+        {
+            "name": "SplitBasedOnLabel",
+            "args": {
+              "field": "model",
+              "label_names": [
+                "pred_class0",
+                "pred_class1"
+              ]
+            }
+        },
+        {
+            "name": "CopyProperties",
+            "args": {
+              "fields": ["pred_class0", "pred_class1", "model"],
+              "from_field": "image",
+              "properties": ["affine"]
+            }
+        }
+    ],
+
+    "writers":
+    [
+      {
+        "name": "WriteNifti",
+        "args": {
+          "field": "model",
+          "dtype": "uint8",
+          "write_path": "{MMAR_EVAL_OUTPUT_PATH}"
+        }
+      },
+      {
+        "name": "WriteNifti",
+        "args":
+        {
+            "field": "pred_class0",
+            "dtype": "uint8",
+            "write_path": "{MMAR_EVAL_OUTPUT_PATH}"
+        }
+      },
+      {
+        "name": "WriteNifti",
+        "args":
+        {
+          "field": "pred_class1",
+          "dtype": "uint8",
+          "write_path": "{MMAR_EVAL_OUTPUT_PATH}"
+        }
+      }
+    ],
+
+    "label_transforms":
+    [
+        {
+            "name": "LoadNifti",
+            "args": {
+              "fields": "label"
+            }
+        },
+        {
+            "name": "ConvertToChannelsFirst",
+            "args": {
+              "fields": "label"
+            }
+        },
+        {
+            "name": "SplitBasedOnLabel",
+            "args": {
+              "field": "label",
+              "label_names": [
+                "label_class0",
+                "label_class1"
+              ]
+            }
+        }
+    ],
+
+    "val_metrics":
+    [
+        {
+            "name": "ComputeAverageDice",
+            "args": {
+              "name": "mean_dice",
+              "field": "pred_class1",
+              "label_field": "label_class1",
+              "report_path": "{MMAR_EVAL_OUTPUT_PATH}"
+            }
+        }
+    ],
+
+    "inferer":
+    {
+        "name": "TFScanWindowInferer",
+        "args": {
+          "roi_size": [160, 160, 160]
+        }
+    },
+
+    "model_loader":
+    {
+        "name": "CheckpointLoader",
+        "args": {
+          "checkpoint_dir": "{MMAR_CKPT_DIR}"
+        }
+    }
+}

admin/transfer/custom_ct_spleen/config/config_fed_client.json

@@ -0,0 +1,58 @@
+{
+    "servers": [
+        {
+            "name": "spleen_segmentation",
+            "service": {
+                "target": "localhost:8002",
+                "options": [
+                    ["grpc.max_send_message_length",    1000000000],
+                    ["grpc.max_receive_message_length", 1000000000]
+                ]
+            }
+        }
+    ],
+    "client": {
+        "local_epochs": 1,
+        "steps_aggregation": 0,
+        "exclude_vars": "(Adam|beta.*power|global_step)",
+        "cross_site_validate": false,
+        "privacy": {
+        },
+        "pre_processors": [
+          {
+              "name": "IteratorNumberGenerator",
+              "args": {
+                  "field": "n_iter"
+              }
+          },
+          {
+            "path": "custom_encryptor.CustomModelEncryptor",
+            "args": {}
+          }
+        ],
+        "post_processors": [
+          {
+            "path": "custom_encryptor.CustomModelDecryptor",
+            "args": {}
+          }
+        ],
+        "req_processors": [
+          {
+            "name": "ClientStatusProcessor"
+          },
+          {
+            "name": "ValidateRequestProcessor"
+          }
+        ],
+        "model_reader_writer": {
+            "name": "TFModelReaderWriter"
+        },
+        "model_validator": {
+            "name": "TFModelValidator"
+        },
+        "retry_timeout": 30,
+        "ssl_private_key": "resources/certs/client1.key",
+        "ssl_cert": "resources/certs/client1.crt",
+        "ssl_root_cert": "resources/certs/rootCA.pem"
+    }
+}

admin/transfer/custom_ct_spleen/config/config_fed_server.json

@@ -0,0 +1,57 @@
+{
+    "servers": [
+        {
+            "name": "spleen_segmentation",
+            "service": {
+                "target": "localhost:8002",
+                "options": [
+                    ["grpc.max_send_message_length",    1000000000],
+                    ["grpc.max_receive_message_length", 1000000000]
+                ]
+            },
+            "max_num_clients": 100,
+            "min_num_clients": 1,
+            "wait_after_min_clients": 10,
+            "heart_beat_timeout": 600,
+            "start_round": 0,
+            "num_rounds": 10,
+            "exclude_vars": "(Adam|beta.*power|global_step)",
+            "num_server_workers": 4
+        }
+    ],
+    "aggregator":
+    {
+      "path": "custom_aggregator.CustomModelAggregator",
+      "args": {
+        "exclude_vars": "(Adam|beta.*power|global_step)"
+      }
+    },
+    "pre_processors": [],
+    "post_processors": [],
+    "model_saver":
+    {
+        "path": "custom_model_saver.CustomModelSaver",
+        "args": {
+          "exclude_vars": "(Adam|beta.*power|global_step)"
+        }
+    },
+    "admin_cmd_modules": [
+      {
+        "name": "TrainingCommandModule"
+      },
+      {
+        "name": "ValidationCommandModule"
+      },
+      {
+        "name": "ShellCommandModule"
+      },
+      {
+        "name": "SystemCommandModule"
+      }
+    ],
+    "result_processors": [
+      {
+        "name": "ValidateResultProcessor"
+      }
+    ]
+}