{
"cells": [
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "view-in-github"
},
"source": [
""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Roboflow 100 - Blood Cell Dataset (BCCD)"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "JFMi8nxJsqct",
"outputId": "ba0118ff-f3b4-42a6-a182-3edd52f369dd"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[?25l \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m0.0/76.7 kB\u001b[0m \u001b[31m?\u001b[0m eta \u001b[36m-:--:--\u001b[0m\r\u001b[2K \u001b[91m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m\u001b[90m╺\u001b[0m\u001b[90m━━\u001b[0m \u001b[32m71.7/76.7 kB\u001b[0m \u001b[31m3.0 MB/s\u001b[0m eta \u001b[36m0:00:01\u001b[0m\r\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m76.7/76.7 kB\u001b[0m \u001b[31m1.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m547.8/547.8 kB\u001b[0m \u001b[31m13.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m178.7/178.7 kB\u001b[0m \u001b[31m17.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m54.5/54.5 kB\u001b[0m \u001b[31m4.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m39.9/39.9 MB\u001b[0m \u001b[31m40.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m116.3/116.3 kB\u001b[0m \u001b[31m9.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m64.9/64.9 kB\u001b[0m \u001b[31m5.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m194.1/194.1 kB\u001b[0m \u001b[31m8.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m134.8/134.8 kB\u001b[0m \u001b[31m10.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25h\u001b[31mERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.\n",
"cudf-cu12 24.4.1 requires pyarrow<15.0.0a0,>=14.0.1, but you have pyarrow 17.0.0 which is incompatible.\n",
"google-colab 1.0.0 requires requests==2.31.0, but you have requests 2.32.3 which is incompatible.\n",
"ibis-framework 8.0.0 requires pyarrow<16,>=2, but you have pyarrow 17.0.0 which is incompatible.\u001b[0m\u001b[31m\n",
"\u001b[0m"
]
}
],
"source": [
"!pip install -q roboflow datasets datasets[vision]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Setup Roboflow connection parameters and configuration BCCD dataset"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "cWyUczWctate",
"outputId": "44c0f011-b3d5-401f-ca39-375c84858499"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"loading Roboflow workspace...\n",
"loading Roboflow project...\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Downloading Dataset Version Zip in /content/coco/ to coco:: 100%|██████████| 9042/9042 [00:01<00:00, 5811.25it/s] "
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"Extracting Dataset Version Zip to /content/coco/ in coco:: 100%|██████████| 372/372 [00:00<00:00, 6072.69it/s]\n",
"Downloading Dataset Version Zip in /content/paligemma/ to paligemma:: 100%|██████████| 7541/7541 [00:01<00:00, 5042.83it/s] "
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"Extracting Dataset Version Zip to /content/paligemma/ in paligemma:: 100%|██████████| 370/370 [00:00<00:00, 5702.03it/s]\n",
"Downloading Dataset Version Zip in /content/florence2_od/ to florence2-od:: 100%|██████████| 7538/7538 [00:01<00:00, 5536.18it/s] "
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"Extracting Dataset Version Zip to /content/florence2_od/ in florence2-od:: 100%|██████████| 372/372 [00:00<00:00, 4983.98it/s]\n"
]
}
],
"source": [
"from google.colab import userdata\n",
"from roboflow import Roboflow\n",
"\n",
"ROBOFLOW_API_KEY = userdata.get('ROBOFLOW_API_KEY')\n",
"rf = Roboflow(api_key=ROBOFLOW_API_KEY)\n",
"\n",
"project = rf.workspace(\"roboflow-100\").project(\"bccd-ouzjz\")\n",
"version = project.version(2)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### select dataset model formats - for models you want to finetune"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"dataset = version.download(model_format=\"paligemma\", location=\"/content/paligemma/\", overwrite=True)\n",
"dataset = version.download(model_format=\"florence2-od\", location=\"/content/florence2_od/\", overwrite=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### validation"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "rtzP2xV9sV52",
"outputId": "6dc6f65b-ac6b-4b85-f452-7d8cc648f562"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"-rw-r--r-- 1 root root 1122675 Jul 23 03:30 coco/train/_annotations.coco.json\n",
"-rw-r--r-- 1 root root 153472 Jul 23 03:30 coco/test/_annotations.coco.json\n",
"-rw-r--r-- 1 root root 314313 Jul 23 03:30 coco/valid/_annotations.coco.json\n",
"-rw-r--r-- 1 root root 21993 Jul 23 03:30 florence2_od/test/annotations.jsonl\n",
"-rw-r--r-- 1 root root 160106 Jul 23 03:30 florence2_od/train/annotations.jsonl\n",
"-rw-r--r-- 1 root root 45081 Jul 23 03:30 florence2_od/valid/annotations.jsonl\n",
"-rw-r--r-- 1 root root 24860 Jul 23 03:30 paligemma/dataset/_annotations.test.jsonl\n",
"-rw-r--r-- 1 root root 180953 Jul 23 03:30 paligemma/dataset/_annotations.train.jsonl\n",
"-rw-r--r-- 1 root root 50942 Jul 23 03:30 paligemma/dataset/_annotations.valid.jsonl\n"
]
}
],
"source": [
"# for each of the dataset model formats (florence2_od / paligemma)\n",
"# do a \"ls -l\" of the json files\n",
"!ls -l florence2_od/test/*.json*\n",
"!ls -l florence2_od/train/*.json*\n",
"!ls -l florence2_od/valid/*.json*\n",
"\n",
"!ls -l paligemma/dataset/*.json*"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "oSgcUrNPu6Xq",
"outputId": "6571f3cf-dd52-4c88-e3a0-de95432caaca"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/content/coco/train: 255 files\n",
"/content/coco/test: 36 files\n",
"/content/coco/valid: 73 files\n",
"/content/florence2_od/test: 36 files\n",
"/content/florence2_od/train: 255 files\n",
"/content/florence2_od/valid: 73 files\n",
"/content/paligemma/dataset: 364 files\n"
]
}
],
"source": [
"import os\n",
"\n",
"def count_jpg_files(directory):\n",
" return len([f for f in os.listdir(directory) if f.endswith('.jpg')])\n",
"\n",
"directories = [\n",
" \"/content/florence2_od/test\",\n",
" \"/content/florence2_od/train\",\n",
" \"/content/florence2_od/valid\",\n",
" \"/content/paligemma/dataset\"\n",
"]\n",
"\n",
"for directory in directories:\n",
" try:\n",
" count = count_jpg_files(directory)\n",
" print(f\"{directory}: {count} files\")\n",
" except FileNotFoundError:\n",
" print(f\"{directory}: Directory not found\")\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Florence 2 - dataset preparation"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"id": "0r7c4TQq9MyS"
},
"outputs": [],
"source": [
"import os\n",
"import json\n",
"from datasets import Dataset, Features, Image, Value, DatasetDict\n",
"\n",
"def load_florence2_annotations(annotation_file, image_dir):\n",
" dataset_entries = []\n",
" with open(annotation_file, 'r') as f:\n",
" for line in f:\n",
" ann = json.loads(line)\n",
" entry = {\n",
" 'image_id': ann['image'],\n",
" 'image': os.path.join(image_dir, ann['image']),\n",
" 'annotations': ann # Keep all original fields\n",
" }\n",
" dataset_entries.append(entry)\n",
" return dataset_entries\n",
"\n",
"# Load annotations\n",
"train_data = load_florence2_annotations('/content/florence2_od/train/annotations.jsonl', '/content/florence2_od/train')\n",
"test_data = load_florence2_annotations('/content/florence2_od/test/annotations.jsonl', '/content/florence2_od/test')\n",
"valid_data = load_florence2_annotations('/content/florence2_od/valid/annotations.jsonl', '/content/florence2_od/valid')\n",
"\n",
"# Define features\n",
"features = Features({\n",
" 'image_id': Value('string'),\n",
" 'image': Image(),\n",
" 'annotations': {\n",
" 'image': Value('string'),\n",
" 'prefix': Value('string'),\n",
" 'suffix': Value('string')\n",
" }\n",
"})\n",
"\n",
"# Create datasets\n",
"florence2_train_dataset = Dataset.from_list(train_data, features=features)\n",
"florence2_test_dataset = Dataset.from_list(test_data, features=features)\n",
"florence2_valid_dataset = Dataset.from_list(valid_data, features=features)\n",
"\n",
"# Combine into a DatasetDict\n",
"florence2_dataset = DatasetDict({\n",
" 'train': florence2_train_dataset,\n",
" 'test': florence2_test_dataset,\n",
" 'validation': florence2_valid_dataset\n",
"})"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### push dataset to hub"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 469,
"referenced_widgets": [
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},
"id": "TTp5OEYU-K2c",
"outputId": "32cbb7dd-47dd-4629-c490-5d48a77980ed"
},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "9062c8deed4745e0a835dcd765112084",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Uploading the dataset shards: 0%| | 0/1 [00:00, ?it/s]"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "60046e1cb9374d3faada7d20d9b49576",
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"version_minor": 0
},
"text/plain": [
"Map: 0%| | 0/255 [00:00, ? examples/s]"
]
},
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},
{
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"version_minor": 0
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"text/plain": [
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"output_type": "display_data"
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"metadata": {},
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"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Dataset splits: dict_keys(['train', 'test', 'validation'])\n",
"Number of training examples: 255\n",
"Number of testing examples: 36\n",
"Number of validation examples: 73\n",
"Features: {'image_id': Value(dtype='string', id=None), 'image': Image(mode=None, decode=True, id=None), 'annotations': {'image': Value(dtype='string', id=None), 'prefix': Value(dtype='string', id=None), 'suffix': Value(dtype='string', id=None)}}\n",
"\n",
"Sample entry:\n",
"{'image_id': 'BloodImage_00343_jpg.rf.d8c56063ce5e40c50efb00a7e0c83c3b.jpg', 'image': , 'annotations': {'image': 'BloodImage_00343_jpg.rf.d8c56063ce5e40c50efb00a7e0c83c3b.jpg', 'prefix': '', 'suffix': 'RBCRBCRBCRBCRBCRBCRBCRBCRBCPlateletsPlateletsWBC'}}\n"
]
}
],
"source": [
"# Push to Hub - uncomment next line when ready to push (update with your id)\n",
"# florence2_dataset.push_to_hub(\"dwb2023/roboflow100-bccd-florence2\")\n",
"\n",
"# Print some information about the dataset\n",
"print(f\"Dataset splits: {florence2_dataset.keys()}\")\n",
"print(f\"Number of training examples: {len(florence2_dataset['train'])}\")\n",
"print(f\"Number of testing examples: {len(florence2_dataset['test'])}\")\n",
"print(f\"Number of validation examples: {len(florence2_dataset['validation'])}\")\n",
"print(f\"Features: {florence2_dataset['train'].features}\")\n",
"\n",
"# Print a sample entry\n",
"print(\"\\nSample entry:\")\n",
"print(florence2_dataset['train'][0])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Paligemma - dataset preparation"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"id": "QAppgYrYDm4a"
},
"outputs": [],
"source": [
"import os\n",
"import json\n",
"from datasets import Dataset, Features, Image, Value, DatasetDict\n",
"\n",
"def load_paligemma_annotations(annotation_file, image_dir):\n",
" dataset_entries = []\n",
" with open(annotation_file, 'r') as f:\n",
" for line in f:\n",
" ann = json.loads(line)\n",
" entry = {\n",
" 'image_id': ann['image'],\n",
" 'image': os.path.join(image_dir, ann['image']),\n",
" 'annotations': ann # Keep all original fields\n",
" }\n",
" dataset_entries.append(entry)\n",
" return dataset_entries\n",
"\n",
"# Load annotations\n",
"train_data = load_paligemma_annotations('/content/paligemma/dataset/_annotations.train.jsonl', '/content/paligemma/dataset')\n",
"test_data = load_paligemma_annotations('/content/paligemma/dataset/_annotations.test.jsonl', '/content/paligemma/dataset')\n",
"valid_data = load_paligemma_annotations('/content/paligemma/dataset/_annotations.valid.jsonl', '/content/paligemma/dataset')\n",
"\n",
"# Define features\n",
"features = Features({\n",
" 'image_id': Value('string'),\n",
" 'image': Image(),\n",
" 'annotations': {\n",
" 'image': Value('string'),\n",
" 'prefix': Value('string'),\n",
" 'suffix': Value('string')\n",
" }\n",
"})\n",
"\n",
"# Create datasets\n",
"paligemma_train_dataset = Dataset.from_list(train_data, features=features)\n",
"paligemma_test_dataset = Dataset.from_list(test_data, features=features)\n",
"paligemma_valid_dataset = Dataset.from_list(valid_data, features=features)\n",
"\n",
"# Combine into a DatasetDict\n",
"paligemma_dataset = DatasetDict({\n",
" 'train': paligemma_train_dataset,\n",
" 'test': paligemma_test_dataset,\n",
" 'validation': paligemma_valid_dataset\n",
"})"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### push dataset to hub"
]
},
{
"cell_type": "code",
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"name": "stdout",
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"text": [
"Dataset splits: dict_keys(['train', 'test', 'validation'])\n",
"Number of training examples: 255\n",
"Number of testing examples: 36\n",
"Number of validation examples: 73\n",
"Features: {'image_id': Value(dtype='string', id=None), 'image': Image(mode=None, decode=True, id=None), 'annotations': {'image': Value(dtype='string', id=None), 'prefix': Value(dtype='string', id=None), 'suffix': Value(dtype='string', id=None)}}\n",
"\n",
"Sample entry:\n",
"{'image_id': 'BloodImage_00327_jpg.rf.dc708dec2caf7249ddca49d41055ca4c.jpg', 'image': , 'annotations': {'image': 'BloodImage_00327_jpg.rf.dc708dec2caf7249ddca49d41055ca4c.jpg', 'prefix': 'detect Platelets ; RBC ; WBC', 'suffix': ' Platelets ; Platelets'}}\n"
]
}
],
"source": [
"# Push to Hub - uncomment next line when ready to push (update with your id)\n",
"# paligemma_dataset.push_to_hub(\"dwb2023/roboflow-bccd-paligemma\")\n",
"\n",
"# Print some information about the dataset\n",
"print(f\"Dataset splits: {paligemma_dataset.keys()}\")\n",
"print(f\"Number of training examples: {len(paligemma_dataset['train'])}\")\n",
"print(f\"Number of testing examples: {len(paligemma_dataset['test'])}\")\n",
"print(f\"Number of validation examples: {len(paligemma_dataset['validation'])}\")\n",
"print(f\"Features: {paligemma_dataset['train'].features}\")\n",
"\n",
"# Print a sample entry\n",
"print(\"\\nSample entry:\")\n",
"print(paligemma_dataset['train'][0])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Compare records across datasets"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"id": "nSiuyM3kKVro"
},
"outputs": [],
"source": [
"# Search for same image across datasets\n",
"image_id_to_find = 'BloodImage_00343_jpg.rf.d8c56063ce5e40c50efb00a7e0c83c3b.jpg'\n",
"\n",
"# Function to find a record by image_id\n",
"def find_record_by_image_id(dataset, image_id):\n",
" for record in dataset['train']:\n",
" if record['image_id'] == image_id:\n",
" return record\n",
" return None"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "-gTVMcLgLiqB",
"outputId": "33c30ff1-a5cc-47e2-f772-2a5e8e5ba585"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Record found: {'image_id': 'BloodImage_00343_jpg.rf.d8c56063ce5e40c50efb00a7e0c83c3b.jpg', 'image': , 'annotations': {'image': 'BloodImage_00343_jpg.rf.d8c56063ce5e40c50efb00a7e0c83c3b.jpg', 'prefix': '', 'suffix': 'RBCRBCRBCRBCRBCRBCRBCRBCRBCPlateletsPlateletsWBC'}}\n"
]
}
],
"source": [
"# Find the Roboflow Florence2 record\n",
"record = find_record_by_image_id(florence2_dataset, image_id_to_find)\n",
"\n",
"# Display the record\n",
"if record:\n",
" print(f\"Record found: {record}\")\n",
"else:\n",
" print(\"Record not found\")"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "D9v-fIxaNUfI",
"outputId": "117fbead-cfa9-48af-abd8-95c7cc979892"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Record found: {'image_id': 'BloodImage_00343_jpg.rf.d8c56063ce5e40c50efb00a7e0c83c3b.jpg', 'image': , 'annotations': {'image': 'BloodImage_00343_jpg.rf.d8c56063ce5e40c50efb00a7e0c83c3b.jpg', 'prefix': 'detect Platelets ; RBC ; WBC', 'suffix': ' RBC ; RBC ; RBC ; RBC ; RBC ; RBC ; RBC ; RBC ; RBC ; Platelets ; Platelets ; WBC'}}\n"
]
}
],
"source": [
"# Find the Roboflow Paligemma record\n",
"record = find_record_by_image_id(paligemma_dataset, image_id_to_find)\n",
"\n",
"# Display the record\n",
"if record:\n",
" print(f\"Record found: {record}\")\n",
"else:\n",
" print(\"Record not found\")"
]
}
],
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"authorship_tag": "ABX9TyOMxc16cMc4VUczcMzaYiLi",
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