path: root/src/e2e.c

#include <stdio.h>
#include <string.h>
#include <math.h>
#include "e2e.h"

uint32_t u32le(const char *src)
{
	uint8_t bytes[4];

	memcpy(bytes, src, 4);

	return (uint32_t)bytes[0]
	       + (((uint32_t)bytes[1]) << 8)
	       + (((uint32_t)bytes[2]) << 16)
	       + (((uint32_t)bytes[3]) << 24);
}

static int make_pointer(const char *start, const char *end,
                        const char *pos, const char **out)
{
	uint32_t ptroffs;

	ptroffs = u32le(pos);

	if (!ptroffs)
		*out = NULL;
	else {
		if (ptroffs > end - start)
			return 1;

		*out = start + ptroffs;
	}

	return 0;
}

#define HEADER_END 36

#define DIRECTORY_NUM_ENTRIES   36
#define DIRECTORY_CURRENT       40
#define DIRECTORY_NEXT          44
#define DIRECTORY_END          52

#define ENTRY_POS          0
#define ENTRY_START        4 
#define ENTRY_SIZE         8
#define ENTRY_PATIENT_ID   16
#define ENTRY_STUDY_ID     20
#define ENTRY_SERIES_ID    24
#define ENTRY_SLICE_ID     28
#define ENTRY_TYPE         36
#define ENTRY_END          44

#define CHUNK_POS          20
#define CHUNK_SIZE         24
#define CHUNK_PATIENT_ID   32
#define CHUNK_STUDY_ID     36
#define CHUNK_SERIES_ID    40
#define CHUNK_SLICE_ID     44
#define CHUNK_IND          48
#define CHUNK_TYPE         52
#define CHUNK_HEADER_END   60

#define DATA_IMAGE  0x40000000

#define IMAGE_SIZE      0
#define IMAGE_TYPE      4
#define IMAGE_WIDTH     12
#define IMAGE_HEIGHT    16
#define IMAGE_IMAGE     20

#define IMAGE_FUNDUS    0x02010201
#define IMAGE_TOMOGRAM  0x02200201

#define UF16_MANTISSA_MASK  ((1 << 11) - 1)  // 10 most significant bits

struct e2e_directory {
	size_t num_entries;
	const char *current, *next;
};

struct e2e_entry {
	const char *start;
	size_t size;

	uint32_t patient_id, study_id, series_id, slice_id, type;
};

struct e2e_chunk {
	const char *origin;
	const struct e2e_entry *entry;

	size_t size;
	uint32_t patient_id, study_id, series_id, slice_id, type;
};

struct e2e_fundus {
	size_t size, width, height;

	uint32_t type;

};

static int read_fundus(const char *start, const char *end, const char *cursor,
                       size_t width, size_t height)
{
	FILE *fp;
	char buffer[1024];

	snprintf(buffer, sizeof(buffer), "out/fundus_%tx.py", cursor - start);
	fp = fopen(buffer, "w");

	fprintf(fp, "data = [\n");
	for (size_t y = 0; y < height; y++) {
		fprintf(fp, "\t[");

		for (size_t x = 0; x < width; x++) {
			uint8_t px;

			memcpy(&px, cursor + y * width + x, 1);
			fprintf(fp, "%s% 3hhu", x ? ", " : "", px);
		}
		fprintf(fp, "]%s\n", y + 1 >= height ? "" : ",");
	}
	fprintf(fp, "]\n");

	fclose(fp);
	return 0;
}

static int read_tomogram(const char *start, const char *end, const char *cursor,
                       size_t width, size_t height)
{
	FILE *fp;
	char buffer[1024];

	snprintf(buffer, sizeof(buffer), "out/tomogram_%tx.py", cursor - start);
	fp = fopen(buffer, "w");

	fprintf(fp, "data = [\n");
	for (size_t y = 0; y < height; y++) {
		fprintf(fp, "\t[");

		for (size_t x = 0; x < width; x++) {
			uint16_t raw;
			int exp, man;
			float px;

			memcpy(&raw, cursor + (y * width + x) * 2, 2);

			man = raw & UF16_MANTISSA_MASK;
			exp = (raw & ~UF16_MANTISSA_MASK) >> 10;

			px = man * exp2f(exp);
			fprintf(fp, "%s%e", x ? ", " : "", px);
		}
		fprintf(fp, "]%s\n", y + 1 >= height ? "" : ",");
	}
	fprintf(fp, "]\n");

	fclose(fp);
	return 0;
}

static int read_image(const char *start, const char *end,
                      const struct e2e_chunk *chunk)
{
	const char *cursor = chunk->origin + CHUNK_HEADER_END;
	size_t size, width, height;
	uint32_t type;

	if (cursor + IMAGE_IMAGE > end) {
		fprintf(stderr, "Image data at %td ends past the end of file.\n",
		        cursor - start);
		return 1;
	}

	size = u32le(cursor + IMAGE_SIZE);
	type = u32le(cursor + IMAGE_TYPE);
	width = u32le(cursor + IMAGE_WIDTH);
	height = u32le(cursor + IMAGE_HEIGHT);

	printf("# %08tx       Image data: %zux%zu, size=%zu\n",
	       cursor - start, width, height, size);
	printf("# Slice is %d\n", chunk->slice_id);
	printf("# Type is %08x\n", type);

	switch (type) {
	case IMAGE_FUNDUS:
		read_fundus(start, end, cursor + IMAGE_IMAGE, width, height);
		break;

	case IMAGE_TOMOGRAM:
		read_tomogram(start, end, cursor + IMAGE_IMAGE, width, height);
		break;
	}

	return 0;
}

static int read_chunk(const char *start, const char *end,
                      const struct e2e_entry *entry, struct e2e_chunk *chunk)
{
	const char *cursor = entry->start, *pos;

	chunk->entry = entry;
	chunk->origin = cursor;

	if (cursor + CHUNK_HEADER_END > end) {
		fprintf(stderr, "Chunk at %td ends past the end of file.\n",
		        cursor - start);
		return 1;
	}

	if (make_pointer(start, end, cursor + CHUNK_POS, &pos)) {
		fprintf(stderr, "Chunk at %td has a bad 'pos' entry.\n",
		        cursor - start);
		return 1;
	}

	if (pos != cursor) {
		fprintf(stderr, "Chunk at %td has a 'pos' entry that differs from the entry's actual position",
		        cursor - start);
		return 1;
	}

	chunk->size = u32le(cursor + CHUNK_SIZE);
	chunk->patient_id = u32le(cursor + CHUNK_PATIENT_ID);
	chunk->study_id = u32le(cursor + CHUNK_STUDY_ID);
	chunk->series_id = u32le(cursor + CHUNK_SERIES_ID);
	chunk->slice_id = u32le(cursor + CHUNK_SLICE_ID);
	chunk->type = u32le(cursor + CHUNK_TYPE);

	return 0;
}

static int read_entry(const char *start, const char *end,
                      const char *cursor, struct e2e_entry *entry)
{
	const char *pos;

	if (cursor + ENTRY_END > end) {
		fprintf(stderr, "Entry at %td ends past the end of file.\n",
		        cursor - start);
		return 1;
	}

	if (make_pointer(start, end, cursor + ENTRY_POS, &pos)) {
		fprintf(stderr, "Entry at %td has a bad 'pos' entry.\n",
		        cursor - start);
		return 1;
	}

	if (pos != cursor) {
		fprintf(stderr, "Entry at %td has a 'pos' entry that differs from the entry's actual position",
		        cursor - start);
		return 1;
	}

	if (make_pointer(start, end, cursor + ENTRY_START, &entry->start)) {
		fprintf(stderr, "Entry at %td has a bad 'start' entry.\n",
		        cursor - start);
		return 1;
	}

	entry->size = u32le(cursor + ENTRY_SIZE);
	entry->patient_id = u32le(cursor + ENTRY_PATIENT_ID);
	entry->study_id = u32le(cursor + ENTRY_STUDY_ID);
	entry->series_id = u32le(cursor + ENTRY_SERIES_ID);
	entry->slice_id = u32le(cursor + ENTRY_SLICE_ID);
	entry->type = u32le(cursor + ENTRY_TYPE);

	return 0;
}

static int read_directory(const char *start, const char *end,
                          const char *cursor, struct e2e_directory *dir)
{
	if (cursor + DIRECTORY_END > end) {
		fprintf(stderr, "Directory at %td ends past the end of file.\n",
		        cursor - start);
		return 1;
	}

	dir->num_entries = u32le(cursor + DIRECTORY_NUM_ENTRIES);

	if (make_pointer(start, end, cursor + DIRECTORY_CURRENT, &dir->current))  {
		fprintf(stderr, "Directory at %td contains a bad 'current' field.\n",
		        cursor - start);
		return 1;
	}

	if (make_pointer(start, end, cursor + DIRECTORY_NEXT, &dir->next))  {
		fprintf(stderr, "Directory at %td contains a bad 'current' field.\n",
		        cursor - start);
		return 1;
	}

	return 0;
}

int e2e_read(const char *start, const char *end)
{
	int rv;
	const char *cursor;

	if (start + HEADER_END > end) {
		fprintf(stderr, "File too short to be an E2E file.\n");
		return 1;
	}

	// TODO: verify the header

	cursor = start + HEADER_END;
	cursor += DIRECTORY_END; // skip the first directory (wtf?)

	while (cursor) {
		struct e2e_directory dir;

		rv = read_directory(start, end, cursor, &dir);
		if (rv)
			return rv;

		printf("# %08tx Directory: num_entries=%zu, current=%08td, next=%td\n",
		       cursor - start, dir.num_entries, dir.current - start,
		       dir.next ? dir.next - start : 0);

		for (size_t i = 0; i < dir.num_entries; i++) {
			const char *entry_cursor;
			struct e2e_entry entry;
			struct e2e_chunk chunk;

			entry_cursor = cursor + DIRECTORY_END + i * ENTRY_END;
			rv = read_entry(start, end, entry_cursor, &entry);
			if (rv)
				return rv;

			printf("# %08tx   Entry %zu: start=%08tx\n",
			       entry_cursor - start, i,
			       entry.start ? entry.start - start : 0);

			if (!entry.start)
				continue;

			rv = read_chunk(start, end, &entry, &chunk);
			if (rv)
				continue;

			printf("# %08tx     Chunk, size=%zu, type=%08x\n",
			       entry.start - start, chunk.size, chunk.type);

			switch (chunk.type) {
			case DATA_IMAGE:
				read_image(start, end, &chunk);
				break;
			}
		}

		cursor = dir.next;
	}

	return 0;
}